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1. Accurate secondary structure prediction and fold recognition for circular dichroism spectroscopy

Author:
Micsonai, András; Wien, Frank; Kernya, Linda; Lee, Young-Ho; Goto, Yuji; Ráéfráéégiers, Matthieu; Kardos, Jáééózsef
Source:
Proceedings of the National Academy of Sciences of the United States of America 2015 v.112 no.24 pp. E3095
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; X-radiation; amyloid; circular dichroism spectroscopy; nuclear magnetic resonance spectroscopy; prediction; topology;     Show all 7 Subjects
Abstract:
... Circular dichroism (CD) spectroscopy is a widely used technique for the study of protein structure. Numerous algorithms have been developed for the estimation of the secondary structure composition from the CD spectra. These methods often fail to provide acceptable results on α/β-mixed or β-structure–rich proteins. The problem arises from the spectral diversity of β-structures, which has hitherto ...
DOI:
10.1073/pnas.1500851112
PubMed:
26038575
PubMed Central:
PMC4475991

2. Folding mechanism of the metastable serpin α1-antitrypsin

Author:
Tsutsui, Yuko; Dela Cruz, Richard; Wintrode, Patrick L.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2012 v.109 no.12 pp. 4467-4472
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; genetic disorders; humans; mass spectrometry; polymerization; protein folding; proteinases;     Show all 7 Subjects
Abstract:
... The misfolding of serpins is linked to several genetic disorders including emphysema, thrombosis, and dementia. During folding, inhibitory serpins are kinetically trapped in a metastable state in which a stretch of residues near the C terminus of the molecule are exposed to solvent as a flexible loop (the reactive center loop). When they inhibit target proteases, serpins transition to a stable sta ...
DOI:
10.1073/pnas.1109125109
PubMed:
22392975
PubMed Central:
PMC3311335

3. Two-dimensional IR spectroscopy and segmental 13C labeling reveals the domain structure of human γD-crystallin amyloid fibrils

Author:
Moran, Sean D.; Woys, Ann Marie; Buchanan, Lauren E.; Bixby, Eli; Decatur, Sean M.; Zanni, Martin T.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2012 v.109 no.9 pp. 3329-3334
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; amyloid; carbon; cataract; crystallins; eye lens; humans; infrared spectroscopy; isotope dilution technique; isotope labeling; models; stable isotopes;     Show all 12 Subjects
Abstract:
... The structural eye lens protein γD-crystallin is a major component of cataracts, but its conformation when aggregated is unknown. Using expressed protein ligation, we uniformly 13C labeled one of the two Greek key domains so that they are individually resolved in two-dimensional (2D) IR spectra for structural and kinetic analysis. Upon acid-induced amyloid fibril formation, the 2D IR spectra reve ...
DOI:
10.1073/pnas.1117704109
PubMed:
22328156
PubMed Central:
PMC3295317

4. Structural flexibility of the Gαs α-helical domain in the β2-adrenoceptor Gs complex

Author:
Westfield, Gerwin H.; Rasmussen, Søren G. F.; Su, Min; Dutta, Somnath; DeVree, Brian T.; Chung, Ka Young; Calinski, Diane; Velez-Ruiz, Gisselle; Oleskie, Austin N.; Pardon, Els; Chae, Pil Seok; Liu, Tong; Li, Sheng; Woods, Virgil L., Jr.; Steyaert, Jan; Kobilka, Brian K.; Sunahara, Roger K.; Skiniotis, Georgios
Source:
Proceedings of the National Academy of Sciences of the United States of America 2011 v.108 no.38 pp. 16086-16091
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; G-proteins; adrenergic receptors; beta-adrenergic agonists; crystal structure; electron microscopy; guanosine diphosphate; molecular models;     Show all 8 Subjects
Abstract:
... The active-state complex between an agonist-bound receptor and a guanine nucleotide-free G protein represents the fundamental signaling assembly for the majority of hormone and neurotransmitter signaling. We applied single-particle electron microscopy (EM) analysis to examine the architecture of agonist-occupied β2-adrenoceptor (β2AR) in complex with the heterotrimeric G protein Gs (Gαsβγ). EM 2D ...
DOI:
10.1073/pnas.1113645108
PubMed:
21914848
PubMed Central:
PMC3179071

5. Schizosacharomyces pombe RNA polymerase II at 3.6-Å resolution

Author:
Spåhr, Henrik; Calero, Guillermo; Bushnell, David A.; Kornberg, Roger D.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2009 v.106 no.23 pp. 9185-9190
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; Schizosaccharomyces pombe; DNA-directed RNA polymerase; crystal structure; X-ray diffraction;     Show all 5 Subjects
Abstract:
... The second structure of a eukaryotic RNA polymerase II so far determined, that of the enzyme from the fission yeast Schizosaccharomyces pombe, is reported here. Comparison with the previous structure of the enzyme from the budding yeast Saccharomyces cerevisiae reveals differences in regions implicated in start site selection and transcription factor interaction. These aspects of the transcription ...
DOI:
10.1073/pnas.0903361106
PubMed:
19458260
PubMed Central:
PMC2684843

6. Bluetongue virus coat protein VP2 contains sialic acid-binding domains, and VP5 resembles enveloped virus fusion proteins

Author:
Zhang, Xing; Boyce, Mark; Bhattacharya, Bishnupriya; Zhang, Xiaokang; Schein, Stan; Roy, Polly; Zhou, Z. Hong
Source:
Proceedings of the National Academy of Sciences of the United States of America 2010 v.107 no.14 pp. 6292-6297
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; coat proteins; sialic acids; Bluetongue virus; electron microscopy; binding proteins; binding sites; viral morphology;     Show all 8 Subjects
Abstract:
... Bluetongue virus (BTV) is transmitted by blood-feeding insects (Culicoides sp.) and causes hemorrhagic diseases in livestock. BTV is a nonenveloped, double-stranded RNA (dsRNA) virus with two capsids: a well-studied, stable core enclosing the dsRNA genome and a highly unstable, poorly studied coat responsible for host cell attachment and entry. Here, based on cryo-electron microscopy (cryoEM), we ...
DOI:
10.1073/pnas.0913403107
PubMed:
20332209
PubMed Central:
PMC2852009

7. Strain-specific sequences required for yeast [PSI⁺] prion propagation

Author:
Chang, Hsiang-Yu; Lin, Jia-Yu; Lee, Han-Chung; Wang, Hui-Ling; King, Chih-Yen
Source:
Proceedings of the National Academy of Sciences of the United States of America 2008 v.105 no.36 pp. 13345-13350
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; protein aggregates; yeasts; Saccharomyces cerevisiae; fungal proteins; nucleotide sequences; amyloid; prions;     Show all 8 Subjects
Abstract:
... Amyloid polymorphism underlies the prion strain phenomenon where a single protein polypeptide adopts different chain-folding patterns to form self-propagating cross-β structures. Three strains of the yeast prion [PSI], namely [VH], [VK], and [VL], have been previously characterized and are amyloid conformers of the yeast translation termination factor Sup35. Here we define specific sequences of th ...
DOI:
10.1073/pnas.0802215105
PubMed:
18757753
PubMed Central:
PMC2533192

8. Membrane binding of Escherichia coli RNase E catalytic domain stabilizes protein structure and increases RNA substrate affinity

Author:
Murashko, Oleg N.; Kaberdin, Vladimir R.; Lin-Chao, Sue
Source:
Proceedings of the National Academy of Sciences of the United States of America 2012 v.109 no.18 pp. 7019-7024
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; Aquifex; Escherichia coli; Haemophilus influenzae; RNA; Synechocystis; active sites; amino acids; cell membranes; circular dichroism spectroscopy; cooling; deoxyribonuclease I; dissociation; electrostatic interactions; enzyme activity; phospholipids; proteins; ribonucleases; surface area;     Show all 19 Subjects
Abstract:
... RNase E plays an essential role in RNA processing and decay and tethers to the cytoplasmic membrane in Escherichia coli; however, the function of this membrane–protein interaction has remained unclear. Here, we establish a mechanistic role for the RNase E–membrane interaction. The reconstituted highly conserved N-terminal fragment of RNase E (NRne, residues 1–499) binds specifically to anionic pho ...
DOI:
10.1073/pnas.1120181109
PubMed:
22509045
PubMed Central:
PMC3344982

9. Structural changes of membrane-anchored native PrPC

Author:
Elfrink, Kerstin; Ollesch, Julian; Stöhr, Jan; Willbold, Dieter; Riesner, Detlev; Gerwert, Klaus
Source:
Proceedings of the National Academy of Sciences of the United States of America 2008 v.105 no.31 pp. 10815-10819
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; Fourier transform infrared spectroscopy; PrPC proteins; humans; lipids; post-translational modification; prion diseases; protein binding; protein folding;     Show all 9 Subjects
Abstract:
... Misfolding and subsequent aggregation of endogeneous proteins constitute essential steps in many human disorders, including Alzheimer and prion diseases. In most prion protein-folding studies, the posttranslational modifications, the lipid anchor in particular, were lacking. Here, we studied a fully posttranslationally modified cellular prion protein, carrying two N-glycosylations and the natural ...
DOI:
10.1073/pnas.0804721105
PubMed:
18669653
PubMed Central:
PMC2504809

10. Amyloid of the prion domain of Sup35p has an in-register parallel β-sheet structure

Author:
Shewmaker, F.; Wickner, R.B.; Tycko, R.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2006 v.103 no.52 pp. 19754-19759
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; Saccharomyces cerevisiae; yeasts; fungal proteins; prions; nuclear magnetic resonance spectroscopy;     Show all 6 Subjects
Abstract:
... The [PSI⁺] prion of Saccharomyces cerevisiae is a self-propagating amyloid form of Sup35p, a subunit of the translation termination factor. Using solid-state NMR we have examined the structure of amyloid fibrils formed in vitro from purified recombinant Sup35¹⁻²⁵³, consisting of the glutamine- and asparagine-rich N-terminal 123-residue prion domain (N) and the adjacent 130-residue highly charged M ...
DOI:
10.1073/pnas.0609638103
PubMed:
17170131
PubMed Central:
PMC1750918

11. Structural basis for rodlet assembly in fungal hydrophobins

Author:
Kwan, A.H.Y.; Winefield, R.D.; Sunde, M.; Matthews, J.M.; Haverkamp, R.G.; Templeton, M.D.; Mackay, J.P.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2006 v.103 no.10 pp. 3621-3626
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; X-ray diffraction; Neurospora crassa; nuclear magnetic resonance spectroscopy; fungal proteins; protein secretion;     Show all 6 Subjects
Abstract:
... Class I hydrophobins are a unique family of fungal proteins that form a polymeric, water-repellent monolayer on the surface of structures such as spores and fruiting bodies. Similar monolayers are being discovered on an increasing range of important microorganisms. Hydrophobin monolayers are amphipathic and particularly robust, and they reverse the wettability of the surface on which they are form ...
DOI:
10.1073/pnas.0505704103
PubMed:
16537446
PubMed Central:
PMC1533775

12. The structure of nucleosome assembly protein 1

Author:
Park, Y.J.; Luger, K.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2006 v.103 no.5 pp. 1248-1253
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; nucleosomes; histones; yeasts; Saccharomyces cerevisiae; binding proteins; molecular chaperones;     Show all 7 Subjects
Abstract:
... Nucleosome assembly protein 1 (NAP-1) is an integral component in the establishment, maintenance, and dynamics of eukaryotic chromatin. It shuttles histones into the nucleus, assembles nucleosomes, and promotes chromatin fluidity, thereby affecting the transcription of many genes. The 3.0 angstrom crystal structure of yeast NAP-1 reveals a previously uncharacterized fold with implications for hist ...
DOI:
10.1073/pnas.0508002103
PubMed:
16432217
PubMed Central:
PMC1345705

13. Strain-specific morphologies of yeast prion amyloid fibrils

Author:
Diaz-Avalos, R.; King, C.Y.; Wall, J.; Simon, M.; Caspar, D.L.D.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2005 v.102 no.29 pp. 10165-10170
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; electron microscopy; yeasts; Saccharomyces cerevisiae; fungal proteins; amyloid; strains; prions;     Show all 8 Subjects
Abstract:
... Mass per length (mpl) measurements on single amyloid fibrils that specifically propagate the [VH], [VK], and [VL] strains of the yeast prion [PSI] reveal unanticipated differences in their structures. Many fibrils have approximately equal to 1.0 prion molecule per 4.7-angstrom cross-beta repeat period, which is consistent with a self-replicating model built by parallel beta-sheet hydrogen-bonding ...
DOI:
10.1073/pnas.0504599102
PubMed:
16006506
PubMed Central:
PMC1177419

14. Juxtaposition of C(2)M and the transverse filament protein C(3)G within the central region of Drosophila synaptonemal complex

Author:
Anderson, L.K.; Royer, S.M.; Page, S.L.; McKim, K.S.; Lai, A.; Lilly, M.A.; Hawley, R.S.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2005 v.102 no.12 pp. 4482-4487
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; nucleoproteins; synaptonemal complex; immunocytochemistry; Drosophila melanogaster; genetic recombination;     Show all 6 Subjects
Abstract:
... The synaptonemal complex (SC) is intimately involved in the process of meiotic recombination in most organisms, but its exact role remains enigmatic. One reason for this uncertainty is that the overall structure of the SC is evolutionarily conserved, but many SC proteins are not. Two putative SC proteins have been identified in Drosophila: C(3)G and C(2)M. Mutations in either gene cause defects in ...
DOI:
10.1073/pnas.0500172102
PubMed:
15767569
PubMed Central:
PMC555515

15. The crystal structure of yeast copper thionein: the solution of a long-lasting enigma

Author:
Calderone, V.; Dolderer, B.; Hartmann, H.J.; Echner, H.; Luchinat, C.; Del Bianco, C.; Mangani, S.; Weser, U.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2005 v.102 no.1 pp. 51-56
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; X-ray diffraction; Saccharomyces cerevisiae; yeasts; metallothionein; crystal structure; copper;     Show all 7 Subjects
Abstract:
... We report here the crystal structure of yeast copper thionein (Cu-MT), determined at 1.44-A resolution. The Cu-MT structure shows the largest known oligonuclear Cu(I) thiolate cluster in biology, consisting of six trigonally and two digonally coordinated Cu(I) ions. This is at variance with the results from previous spectroscopic determinations, which were performed on MT samples containing seven ...
DOI:
10.1073/pnas.0408254101
PubMed:
15613489
PubMed Central:
PMC544076

16. Crystal structure and activities of EXPB1 (Zea m 1), a β-expansin and group-1 pollen allergen from maize

Author:
Yennawar, N.H.; Li, L.C.; Dudzinski, D.M.; Tabuchi, A.; Cosgrove, D.J.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2006 v.103 no.40 pp. 14664-14671
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; Zea mays; X-ray diffraction; xylan; crystal structure; cell walls; corn; allergens; expansins; pollen; binding capacity;     Show all 11 Subjects
Abstract:
... Expansins are small extracellular proteins that promote turgor-driven extension of plant cell walls. EXPB1 (also called Zea m 1) is a member of the β-expansin subfamily known in the allergen literature as group-1 grass pollen allergens. EXPB1 induces extension and stress relaxation of grass cell walls. To help elucidate expansin's mechanism of wall loosening, we determined the structure of EXPB1 b ...
DOI:
10.1073/pnas.0605979103
PubMed:
16984999
PubMed Central:
PMC1595409

17. Crystal structure and activity of Bacillus subtilis YoaJ (EXLX1), a bacterial expansin that promotes root colonization

Author:
Kerff, Frédéric; Amoroso, Ana; Herman, Raphaël; Sauvage, Eric; Petrella, Stéphanie; Filée, Patrice; Charlier, Paulette; Joris, Bernard; Tabuchi, Akira; Nikolaidis, Nikolas; Cosgrove, Daniel J.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2008 v.105 no.44 pp. 16876-16881
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; coleoptiles; bacterial colonization; crystal structure; cell walls; wheat; cellulose; expansins; bacterial proteins; Bacillus subtilis; Triticum aestivum; binding capacity; roots;     Show all 13 Subjects
Abstract:
... We solved the crystal structure of a secreted protein, EXLX1, encoded by the yoaJ gene of Bacillus subtilis. Its structure is remarkably similar to that of plant β-expansins (group 1 grass pollen allergens), consisting of 2 tightly packed domains (D1, D2) with a potential polysaccharide-binding surface spanning the 2 domains. Domain D1 has a double-ψ β-barrel fold with partial conservation of the ...
DOI:
10.1073/pnas.0809382105
PubMed:
18971341
PubMed Central:
PMC2579346

18. Prion protein NMR structures of cats, dogs, pigs, and sheep

Author:
Lysek, D.A.; Schorn, C.; Nivon, L.G.; Esteve-Moya, V.; Christen, B.; Calzolai, L.; Schroetter, C. von.; Fiorito, F.; Herrmann, T.; Guntert, P.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2005 v.102 no.3 pp. 640-645
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; prions; nuclear magnetic resonance spectroscopy; cats; dogs; swine; sheep; protein isoforms; amino acid sequences; sequence alignment;     Show all 10 Subjects
Abstract:
... The NMR structures of the recombinant cellular form of the prion proteins (PrP(C)) of the cat (Felis catus), dog (Canis familiaris), and pig (Sus scrofa), and of two polymorphic forms of the prion protein from sheep (Ovis aries) are presented. In all of these species, PrP(C) consists of an N-terminal flexibly extended tail with approximately 100 amino acid residues and a C-terminal globular domain ...
DOI:
10.1073/pnas.0408937102
PubMed:
15647367
PubMed Central:
PMC545531

19. Prion protein NMR structures of chickens, turtles, and frogs

Author:
Calzolai, L.; Lysek, D.A.; Perez, D.R.; Guntert, P.; Wuthrich, K.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2005 v.102 no.3 pp. 651-655
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; prions; nuclear magnetic resonance spectroscopy; chickens; Trachemys scripta; turtles; Xenopus laevis; amino acid sequences;     Show all 8 Subjects
Abstract:
... The NMR structures of the recombinant prion proteins from chicken (Gallus gallus; chPrP), the red-eared slider turtle (Trachemys scripta; tPrP), and the African clawed frog (Xenopus laevis; xlPrP) are presented. The amino acid sequences of these prion proteins show approximately 30% identity with mammalian prion proteins. All three species form the same molecular architecture as mammalian PrP(C), ...
DOI:
10.1073/pnas.0408939102
PubMed:
15647366
PubMed Central:
PMC545536

20. The molecular structure of spider dragline silk: folding and orientation of the protein backbone

Author:
Beek, J.D. van.; Hess, S.; Vollrath, F.; Meier, B.H.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2002 v.99 no.16 pp. 10266-10271
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; Nephila; silk; molecular conformation; nuclear magnetic resonance spectroscopy;     Show all 5 Subjects
Abstract:
... The design principles of spider dragline silk, nature's high-performance fiber, are still largely unknown, in particular for the noncrystalline glycine-rich domains, which form the bulk of the material. Here we apply two-dimensional solid-state NMR to determine the distribution of the backbone torsion angles (phi,psi) as well as the orientation of the polypeptide backbone toward the fiber at both ...
DOI:
10.1073/pnas.152162299
PubMed:
12149440
PubMed Central:
PMC124902

21. Eight novel families of miniature inverted repeat transposable elements in the African malaria mosquito, Anopheles gambiae

Author:
Tu, Z.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2001 v.98 no.4 pp. 1699-1704
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; genome; mutation; Anopheles gambiae; DNA conformation; transposons; gene dosage;     Show all 7 Subjects
DOI:
10.1073/pnas.98.4.1699
PubMed:
11172014
PubMed Central:
PMC29320

22. Positive charge is an important feature of the C-terminal transport signal of the VirB/D4-translocated proteins of Agrobacterium

Author:
Vergunst, A.C.; Lier, M.C.M. van; Dulk-Ras, A. den; Grosse Stuve, T.A.; Ouwehand, A.; Hooykaas, P.J.J.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2005 v.102 no.3 pp. 832-837
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; Arabidopsis thaliana; genetic transformation; Agrobacterium radiobacter; transfer DNA; bacterial diseases of plants; protein transport; bacterial proteins; signal peptide; DNA-binding proteins; site-directed mutagenesis; virulence;     Show all 12 Subjects
Abstract:
... Several human pathogens and the plant pathogen Agrobacterium tumefaciens use a type IV secretion system for translocation of effector proteins into host cells. How effector proteins are selected for transport is unknown, but a C-terminal transport signal is present in the proteins translocated by the A. tumefaciens VirB/D4 type IV secretion system. We characterized this signal in the virulence pro ...
DOI:
10.1073/pnas.0406241102
PubMed:
15644442
PubMed Central:
PMC545537

23. Binding of elongin A or a von Hippel-Lindau peptide stabilizes the structure of yeast elongin C

Author:
Botuyan, M.V.; Koth, C.M.; Mer, G.; Chakrabartty, A.; Conaway, J.W.; Conaway, R.C.; Edwards, A.M.; Arrowsmith, C.H.; Chazin, W.J.
Source:
Proceedings of the National Academy of Sciences of the United States of America 1999 v.96 no.16 pp. 9033-9038
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; Saccharomyces cerevisiae; transcription factors; peptides; molecular conformation; dissociation; nuclear magnetic resonance spectroscopy;     Show all 7 Subjects
Abstract:
... Elongin is a heterotrimeric transcription elongation factor composed of subunits A, B, and C in mammals. Elongin A and C are F-box-containing and SKP1 homologue proteins, respectively, and are therefore of interest for their potential roles in cell cycle-dependent proteolysis. Mammalian elongin C interacts with both elongin A and elongin B, as well as with the von Hippel-Lindau tumor suppressor pr ...
DOI:
10.1073/pnas.96.16.9033
PubMed:
10430890
PubMed Central:
PMC17727

24. Evolution of a light-harvesting protein by addition of new subunits and rearrangement of conserved elements: crystal structure of a cryptophyte phycoerythrin at 1.63-angstrom resolution

Author:
Wilk, K.E.; Harrop, S.J.; Jankova, L.; Edler, D.; Keenan, G.; Sharples, F.; Hiller, R.G.; Curmi, P.M.G.
Source:
Proceedings of the National Academy of Sciences of the United States of America 1999 v.96 no.16 pp. 8901-8906
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; X-ray diffraction; algae; light harvesting complex; crystals; Rhodomonas; molecular conformation;     Show all 7 Subjects
Abstract:
... Cryptophytes are unicellular photosynthetic algae that use a lumenally located light-harvesting system, which is distinct from the phycobilisome structure found in cyanobacteria and red algae. One of the key components of this system is water-soluble phycoerythrin (PE) 545 whose expression is enhanced by low light levels. The crystal structure of the heterodimeric alpha(1)alpha(2)betabeta PE 545 f ...
DOI:
10.1073/pnas.96.16.8901

25. NMR structure reveals intramolecular regulation mechanism for pheromone binding and release

Author:
Horst, R.; Damberger, F.; Luginbuhl, P.; Guntert, P.; Peng, G.; Nikonova, L.; Leal, W.S.; Wuthrich, K.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2001 v.98 no.25 pp. 14374-14379
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; Bombyx mori; binding proteins; receptors; pheromones; molecular conformation; pH; nuclear magnetic resonance spectroscopy; binding sites;     Show all 9 Subjects
Abstract:
... Odorants are transmitted by small hydrophobic molecules that cross the aqueous sensillar lymph surrounding the dendrites of the olfactory neurons to stimulate the olfactory receptors. In insects, the transport of pheromones, which are a special class of odorants, is mediated by pheromone-binding proteins (PBPs), which occur at high concentrations in the sensillar lymph. The PBP from the silk moth ...
DOI:
10.1073/pnas.251532998
PubMed:
11724947
PubMed Central:
PMC64689

26. Crystal structure of the regulatory subunit H of the V-type ATPase of Saccharomyces cerevisiae

Author:
Sagermann, M.; Stevens, T.H.; Matthews, B.W.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2001 v.98 no.13 pp. 7134-7139
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; X-ray diffraction; Saccharomyces cerevisiae; adenosinetriphosphatase; vacuoles; tonoplast; crystals; molecular conformation; amino acid sequences;     Show all 9 Subjects
Abstract:
... In contrast to the F-type ATPases, which use a proton gradient to generate ATP, the V-type enzymes use ATP to actively transport protons into organelles and extracellular compartments. We describe here the structure of the H-subunit (also called Vma13p) of the yeast enzyme. This is the first structure of any component of a V-type ATPase. The H-subunit is not required for assembly but plays an esse ...
DOI:
10.1073/pnas.131192798
PubMed:
11416198
PubMed Central:
PMC34635

27. Origin of a chloroplast protein importer

Author:
Bolter, B.; Soll, J.; Schulz, A.; Hinnah, S.; Wagner, R.
Source:
Proceedings of the National Academy of Sciences of the United States of America 1998 v.95 no.26 pp. 15831-15836
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; proteins; Synechocystis; protein transport; electric current; electrophysiology; lipid bilayers; molecular conformation; immunocytochemistry;     Show all 9 Subjects
Abstract:
... During evolution, chloroplasts have relinquished the majority of their genes to the nucleus. The products of transferred genes are imported into the organelle with the help of an import machinery that is distributed across the inner and outer plastid membranes. The evolutionary origin of this machinery is puzzling because, in the putative predecessors, the cyanobacteria, the outer two membranes, t ...
DOI:
10.1073/pnas.95.26.15831
PubMed:
9861056
PubMed Central:
PMC28130

28. Deleterious mutations destabilize ribosomal RNA in endosymbiotic bacteria

Author:
Lambert, J.D.; Moran, N.A.
Source:
Proceedings of the National Academy of Sciences of the United States of America 1998 v.95 no.8 pp. 4458-4462
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; bacteria; symbionts; Wolbachia pipientis; insect pests; ribosomal RNA; phylogeny; mutation;     Show all 8 Subjects
Abstract:
... In populations that are small and asexual, mutations with slight negative effects on fitness will drift to fixation more often than in large or sexual populations in which they will be eliminated by selection. If such mutations occur in substantial numbers, the combined effects of long-term asexuality and small population size may result in substantial accumulation of mildly deleterious substituti ...
DOI:
10.1073/pnas.95.8.4458
PubMed:
9539759
PubMed Central:
PMC22511

29. Global flexibility of tertiary structure in RNA: yeast tRNA(Phe) as a model system

Author:
Friederich, M.W.; Vacano, E.; Hagerman, P.J.
Source:
Proceedings of the National Academy of Sciences of the United States of America 1998 v.95 no.7 pp. 3572-3577
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; Saccharomyces cerevisiae; transfer RNA; phenylalanine; molecular conformation; magnesium; electrophoresis; electrical properties;     Show all 8 Subjects
Abstract:
... The study of RNA structure using x-ray crystallography or NMR has yielded a wealth of detailed structural information; however, such approaches do not generally yield quantitative information regarding long-range flexibility in solution. To address this issue, we describe a solution-based method that is capable of characterizing the global flexibilities of nonhelix elements in RNA, provided that s ...
DOI:
10.1073/pnas.95.7.3572
PubMed:
9520407
PubMed Central:
PMC19877

30. A novel type of RNA editing occurs in the mitochondrial tRNAs of the centipede Lithobius forficatus

Author:
Lavrov, D.V.; Brown, W.M.; Boore, J.L.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2000 v.97 no.25 pp. 13738-13742
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; RNA editing; mitochondrial DNA; nucleotide sequences; transfer RNA; genes; complementary DNA; molecular conformation; genomics; Lithobius forficatus;     Show all 10 Subjects
DOI:
10.1073/pnas.250402997
PubMed:
11095730
PubMed Central:
PMC17645

31. Light stress-regulated two-helix proteins in Arabidopsis thaliana related to the chlorophyll a/b-binding gene family

Author:
Heddad, M.; Adamska, I.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2000 v.97 no.7 pp. 3741-3746
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; Arabidopsis thaliana; nucleotide sequences; amino acid sequences; molecular conformation; gene expression; light intensity; messenger RNA; cytochemistry; thylakoids;     Show all 10 Subjects
Abstract:
... The chlorophyll a/b, chlorophyll a/c, and chlorophyll a/a light-harvesting proteins are part of an extended gene family that also includes the transiently expressed stress proteins, the Elips (early light-induced proteins). Four Elip homologue proteins, encoded by single-copy nuclear genes, have been identified in the Arabidopsis thaliana database. These proteins were divided into two groups accor ...
DOI:
10.1073/pnas.97.7.3741
PubMed:
10725357
PubMed Central:
PMC16310

32. Did homeodomain proteins duplicate before the origin of angiosperms, fungi, and metazoa?

Author:
Bharathan, G.; Janssen, B.J.; Kellogg, E.A.; Sinha, N.
Source:
Proceedings of the National Academy of Sciences of the United States of America 1997 v.94 no.25 pp. 13749-13753
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; transcription factors; animals; phylogeny; genes; DNA-binding domains; Angiospermae; molecular conformation; fungi;     Show all 9 Subjects
Abstract:
... Homeodomain proteins are transcription factors that play a critical role in early development in eukaryotes. These proteins previously have been classified into numerous subgroups whose phylogenetic relationships are unclear. Our phylogenetic analysis of representative eukaryotic sequences suggests that there are two major groups of homeodomain proteins, each containing sequences from angiosperms, ...
DOI:
10.1073/pnas.94.25.13749
PubMed:
9391098
PubMed Central:
PMC28378

33. Intron self-complementarity enforces exon inclusion in a yeast pre-mRNA

Author:
Howe, K.J.; Ares, M. Jr.
Source:
Proceedings of the National Academy of Sciences of the United States of America 1997 v.94 no.23 pp. 12467-12472
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; messenger RNA; alternative splicing; mutation; Saccharomyces cerevisiae; introns; molecular conformation;     Show all 7 Subjects
Abstract:
... Skipping of internal exons during removal of introns from pre-mRNA must be avoided for proper expression of most eukaryotic genes. Despite significant understanding of the mechanics of intron removal, mechanisms that ensure inclusion of internal exons in multi-intron pre-mRNAs remain mysterious. Using a natural two-intron yeast gene, we have identified distinct RNA-RNA complementarities within eac ...
DOI:
10.1073/pnas.94.23.12467
PubMed:
9356473
PubMed Central:
PMC25003

34. Prion-inducing domain 2-114 of yeast Sup35 protein transforms in vitro into amyloid-like filaments

Author:
King, C.Y.; Tittmann, P.; Gross, H.; Gebert, R.; Aebi, M.; Wuthrich, K.
Source:
Proceedings of the National Academy of Sciences of the United States of America 1997 v.94 no.13 pp. 6618-6622
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; Saccharomyces cerevisiae; prions; molecular conformation; cell structures; amyloid;     Show all 6 Subjects
Abstract:
... The yeast non-Mendelian genetic factor [PSI], which enhances the efficiency of tRNA-mediated non-sense suppression in Saccharomyces cerevisiae, is thought to be an abnormal cellular isoform of the Sup35 protein. Genetic studies have established that the N-terminal part of the Sup35 protein is sufficient for the genesis as well as the maintenance of [PSI]. Here we demonstrate that the N-terminal po ...
DOI:
10.1073/pnas.94.13.6618
PubMed:
9192614
PubMed Central:
PMC21207

35. Thermal unfolding of human high-density apolipoprotein A-1: implications for a lipid-free molten globular state

Author:
Gursky, O.; Atkinson, D.
Source:
Proceedings of the National Academy of Sciences of the United States of America 1996 v.93 no.7 pp. 2991-2995
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; enthalpy; humans; apolipoproteins; protein tertiary structure; differential scanning calorimetry; molecular conformation; spectroscopy;     Show all 8 Subjects
Abstract:
... Apolipoprotein A-1 (apoA-1) in complex with high-density lipoprotein is critically involved in the transport and metabolism of cholesterol and in the pathogenesis of atherosclerosis. We reexamined the thermal unfolding of lipid-free apoA-1 in low-salt solution at pH approximately 7, by using differential scanning calorimetry and circular dichroism. At protein concentrations < 5 mg/ml, thermal unfo ...
DOI:
10.1073/pnas.93.7.2991
PubMed:
8610156
PubMed Central:
PMC39748

36. Arterivirus discontinuous mRNA transcription is guided by base pairing between sense and antisense transcription-regulating sequences

Author:
Marle, G. van.; Dobbe, J.C.; Gultyaev, A.P.; Luytjes, W.; Spaan, W.J.M.; Snijder, E.J.
Source:
Proceedings of the National Academy of Sciences of the United States of America 1999 v.96 no.21 pp. 12056-12061
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; messenger RNA; complementary DNA; Equine arteritis virus; clones; transcription (genetics); nucleotide sequences; site-directed mutagenesis; molecular conformation;     Show all 9 Subjects
Abstract:
... To generate an extensive set of subgenomic (sg) mRNAs, nidoviruses (arteriviruses and coronaviruses) use a mechanism of discontinuous transcription. During this process, mRNAs are generated that represent the genomic 5' sequence, the so-called leader RNA, fused at specific positions to different 3' regions of the genome. The fusion of the leader to the mRNA bodies occurs at a short, conserved sequ ...
DOI:
10.1073/pnas.96.21.12056
PubMed:
10518575
PubMed Central:
PMC18411

37. Evidence that a plant virus switched hosts to infect a vertebrate and then recombined with a vertebrate-infecting virus

Author:
Gibbs, M.J.; Weiller, G.F.
Source:
Proceedings of the National Academy of Sciences of the United States of America 1999 v.96 no.14 pp. 8022-8027
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; plant viruses; Caliciviridae; replication origin; phylogeny; amino acid sequences; viral proteins; Porcine circovirus; molecular conformation; genetic recombination;     Show all 10 Subjects
Abstract:
... There are several similarities between the small, circular, single-stranded-DNA genomes of circoviruses that infect vertebrates and the nanoviruses that infect plants. We analyzed circovirus and nanovirus replication initiator protein (Rep) sequences and confirmed that an N-terminal region in circovirus Reps is similar to an equivalent region in nanovirus Reps. However, we found that the remaining ...
DOI:
10.1073/pnas.96.14.8022
PubMed:
10393941
PubMed Central:
PMC22181

38. Structure, thermostability, and conformational flexibility of hen egg-white lysozyme dissolved in glycerol

Author:
Knubovets, T.; Osterhout, J.J.; Connolly, P.J.; Klibanov, A.M.
Source:
Proceedings of the National Academy of Sciences of the United States of America 1999 v.96 no.4 pp. 1262-1267
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; lysozyme; nuclear magnetic resonance spectroscopy; heat stability; protein tertiary structure; glycerol; spectral analysis; molecular conformation; egg albumen;     Show all 9 Subjects
Abstract:
... Hen egg-white lysozyme dissolved in glycerol containing 1% water was studied by using CD and amide proton exchange monitored by two-dimensional 1H NMR. The far- and near-UV CD spectra of the protein showed that the secondary and tertiary structures of lysozyme in glycerol were similar to those in water. Thermal melting of lysozyme in glycerol followed by CD spectral changes indicated unfolding of ...
DOI:
10.1073/pnas.96.4.1262
PubMed:
9990012
PubMed Central:
PMC15451

39. U1 small nuclear RNA and spliceosomal introns in Euglena gracilis

Author:
Breckenridge, D.G.; Watanabe, Y.; Greenwood, S.J.; Gray, M.W.; Schnare, M.N.
Source:
Proceedings of the National Academy of Sciences of the United States of America 1999 v.96 no.3 pp. 852-856
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; proteins; messenger RNA; alternative splicing; structural genes; complementary DNA; small nuclear RNA; molecular conformation; introns; Euglena gracilis;     Show all 10 Subjects
Abstract:
... In the flagellated protozoon Euglena gracilis, characterized nuclear genes harbor atypical introns that usually are flanked by short repeats, adopt complex secondary structures in pre-mRNA, and do not obey the GT-AG rule of conventional cis-spliced introns. In the nuclear fibrillarin gene of E. gracilis, we have identified three spliceosomal-type introns that have GT-AG consensus borders. Furtherm ...
DOI:
10.1073/pnas.96.3.852
PubMed:
9927657
PubMed Central:
PMC15314

40. Mg-SINE: a short interspersed nuclear element from the rice blast fungus, Magnaporthe grisea

Author:
Kachroo, P.; Leong, S.A.; Chattoo, B.B.
Source:
Proceedings of the National Academy of Sciences of the United States of America 1995 v.92 no.24 pp. 11125-11129
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; Southern blotting; messenger RNA; Magnaporthe grisea; DNA conformation; Northern blotting; transposons;     Show all 7 Subjects
Abstract:
... A short interspersed nuclear element, Mg-SINE, was isolated and characterized from the genome of the rice blast fungus, Magnaporthe grisea. Mg-SINE was isolated as an insertion element within Pot2, an inverted-repeat transposon from M. grisea and shows typical features of a mammalian SINE. Mg-SINE is present as a 0.47-kb interspersed sequence at approximately 100 copies per haploid genome in both ...
DOI:
10.1073/pnas.92.24.11125
PubMed:
7479950
PubMed Central:
PMC40584

41. Crystal structure of the cell cycle-regulatory protein suc1 reveals a beta-hinge conformational switch

Author:
Bourne, Y.; Arvai, A.S.; Bernstein, S.L.; Watson, M.H.; Reed, S.I.; Endicott, J.E.; Nobel, M.E.; Johnson, L.N.; Tainer, J.A.
Source:
Proceedings of the National Academy of Sciences of the United States of America 1995 v.92 no.22 pp. 10232-10236
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; X-ray diffraction; Saccharomycetales; proteins; molecular conformation; Schizosaccharomyces pombe;     Show all 6 Subjects
Abstract:
... The Schizosaccharomyces pombe cell cycle-regulatory protein suc1, named as the suppressor of cdc2 temperature-sensitive mutations, is essential for cell cycle progression. To understand suc1 structure-function relationships and to help resolve conflicting interpretations of suc1 function based on genetic studies of suc1 and its functional homologs in both lower and higher eukaryotes, we have deter ...
DOI:
10.1073/pnas.92.22.10232
PubMed:
7479758
PubMed Central:
PMC40770

42. Prediction of protein folding class using global description of amino acid sequence

Author:
Dubchak, I.; Muchnik, I.; Holbrook, S.R.; Kim, S.H.
Source:
Proceedings of the National Academy of Sciences of the United States of America 1995 v.92 no.19 pp. 8700-8704
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; proteins; molecular conformation; amino acid sequences; prediction; computer analysis; hydrophobicity; solvents; neural networks;     Show all 9 Subjects
Abstract:
... We present a method for predicting protein folding class based on global protein chain description and a voting process. Selection of the best descriptors was achieved by a computer-simulated neural network trained on a data base consisting of 83 folding classes. Protein-chain descriptors include overall composition, transition, and distribution of amino acid attributes, such as relative hydrophob ...
DOI:
10.1073/pnas.92.19.8700
PubMed:
7568000
PubMed Central:
PMC41034

43. On the existence and implications of an inverse folding code in proteins

Author:
Rackovsky, S.
Source:
Proceedings of the National Academy of Sciences of the United States of America 1995 v.92 no.15 pp. 6861-6863
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; proteins; amino acid sequences; molecular conformation; protein folding;     Show all 5 Subjects
Abstract:
... The existence of a code relating the set of possible sequences at a given position in a protein backbone to the local structure at that location is investigated. It is shown that only 73% of 4-C alpha structure fragments in a sample of 114 protein structures exhibit a preference for a particular set of sequences. The remaining structures can accommodate essentially any sequence. The structures tha ...
DOI:
10.1073/pnas.92.15.6861
PubMed:
7624332
PubMed Central:
PMC41429

44. An A-DNA triplet code: thermodynamic rules for predicting A- and B-DNA

Author:
Basham, B.; Schroth, G.P.; Ho, P.S.
Source:
Proceedings of the National Academy of Sciences of the United States of America 1995 v.92 no.14 pp. 6464-6468
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; DNA; nucleotide sequences; prediction; thermodynamics; energy; DNA conformation; spectroscopy;     Show all 8 Subjects
Abstract:
... The ability to predict macromolecular conformations from sequence and thermodynamic principles has long been coveted but generally has not been achieved. We show that differences in the hydration of DNA surfaces can be used to distinguish between sequences that form A- and B-DNA. From this, a "triplet code" of A-DNA propensities was derived as energetic rules for predicting A-DNA formation. This c ...
DOI:
10.1073/pnas.92.14.6464
PubMed:
7604014
PubMed Central:
PMC41538

45. Circular dichrosim, molecular modeling, and serology indicate that the structural basis of antigenic variation in foot-and-mouth disease virus is alpha-helix formation

Author:
France, L.L.; Piatti, P.G.; Newman, J.F.E.; Toth, I.; Gibbons, W.A.; Brown, F.
Source:
Proceedings of the National Academy of Sciences of the United States of America 1994 v.91 no.18 pp. 8442-8446
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; Aphthovirus; viral proteins; molecular conformation; antigenic variation; synthetic peptides; epitopes; spectroscopy; viral antigens;     Show all 9 Subjects
Abstract:
... Seven antigenic variants obtained from a single field isolate of foot-and-mouth disease virus, serotype A12, differ only at residues 148 and 153 in the immunodominant loop of viral protein VP1. Synthetic peptides corresponding to the region 141-160 are highly immunogenic. UV circular dichroism shows that (i) in aqueous solution the peptides are nearly identical, but in 100% trifluoroethanol they d ...
DOI:
10.1073/pnas.91.18.8442

46. A conserved stem-loop structure in the 3' untranslated region of procyclin mRNAs regulates expression in Trypanosoma brucei

Author:
Hehl, A.; Vassella, E.; Braun, R.; Roditi, I.
Source:
Proceedings of the National Academy of Sciences of the United States of America 1994 v.91 no.1 pp. 370-374
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; Trypanosoma brucei; messenger RNA; molecular conformation; microbial proteins; developmental stages; gene expression;     Show all 7 Subjects
Abstract:
... African trypanosomes that cycle between mammalian hosts and the tsetse fly vector must be poised to survive in different environments. The control of stage-specific gene expression is undoubtedly one of the keys to successful adaptation, but no regulatory elements have been defined to date. Procyclins (also known as procyclic acidic repetitive proteins) are specifically expressed on the surface of ...
DOI:
10.1073/pnas.91.1.370
PubMed:
8278396
PubMed Central:
PMC42949

47. Recombinant scrapie-like prion protein of 106 amino acids is soluble

Author:
Muramoto, T.; Scott, M.; Cohen, F.E.; Prusiner, S.B.
Source:
Proceedings of the National Academy of Sciences of the United States of America 1996 v.93 no.26 pp. 15457-15462
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; neurons; animal proteins; recombinant proteins; PrPSc proteins; transgenic animals; mice; solubility; detergents; molecular conformation;     Show all 10 Subjects
Abstract:
... The N terminus of the scrapie isoform of prion protein (PrP(Sc)) can be truncated without loss of scrapie infectivity and, correspondingly, the truncation of the N terminus of the cellular isoform, PrP(C), still permits conversion into PrP(Sc). To assess whether additional segments of the PrP molecule can be deleted, we previously removed regions of putative secondary structure in PrP(C); in the p ...
DOI:
10.1073/pnas.93.26.15457
PubMed:
8986833
PubMed Central:
PMC26426

48. RNA editing in Arabidopsis mitochondria effects 441 C to U changes in ORFs

Author:
Giege, P.; Brennicke, A.
Source:
Proceedings of the National Academy of Sciences of the United States of America 1999 v.96 no.26 pp. 15324-15329
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; Arabidopsis thaliana; messenger RNA; complementary DNA; open reading frames; mitochondrial DNA; codons; mitochondria; hydrophobicity; RNA editing; molecular conformation; plant proteins;     Show all 12 Subjects
Abstract:
... On the basis of the sequence of the mitochondrial genome in the flowering plant Arabidopsis thaliana, RNA editing events were systematically investigated in the respective RNA population. A total of 456 C to U, but no U to C, conversions were identified exclusively in mRNAs, 441 in ORFs, 8 in introns, and 7 in leader and trailer sequences. No RNA editing was seen in any of the rRNAs or in several ...
DOI:
10.1073/pnas.96.26.15324
PubMed:
10611383
PubMed Central:
PMC24818

49. A transcriptional activating region with two contrasting modes of protein interaction

Author:
Ansari, A.Z.; Reece, R.J.; Ptashne, M.
Source:
Proceedings of the National Academy of Sciences of the United States of America 1998 v.95 no.23 pp. 13543-13548
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; Saccharomyces cerevisiae; transcription factors; DNA-binding proteins; cysteine; proline; mutants; molecular conformation; gene expression; reporter genes; beta-galactosidase; transcription (genetics); binding sites; site-directed mutagenesis;     Show all 14 Subjects
Abstract:
... A C-terminal segment of the yeast activator Gal4 manifests two functions: When tethered to DNA, it elicits gene activation, and it binds the inhibitor Gal80. Here we examine the effects on these two functions of cysteine and proline substitutions. We find that, although certain cysteine substitutions diminish interaction with Gal80, those substitutions have little effect on the activating function ...
DOI:
10.1073/pnas.95.23.13543
PubMed:
9811836
PubMed Central:
PMC24855

50. SIRE-1, a copia/Ty1-like retroelement from soybean, encodes a retroviral envelope-like protein

Author:
Laten, H.M.; Majumdar, A.; Gaucher, E.A.
Source:
Proceedings of the National Academy of Sciences of the United States of America 1998 v.95 no.12 pp. 6897-6902
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; RNA-directed DNA polymerase; retrotransposons; Glycine max; Retroviridae; transmembrane proteins; open reading frames; amino acid sequences; molecular conformation;     Show all 9 Subjects
Abstract:
... The soybean genome hosts a family of several hundred, relatively homogeneous copies of a large, copia/Ty1-like retroelement designated SIRE-1. A copy of this element has been recovered from a Glycine max genomic library. DNA sequence analysis of two SIRE-1 subclones revealed that SIRE-1 contains a long, uninterrupted, ORF between the 3' end of the pol ORF and the 3' long terminal repeat (LTR), a r ...
DOI:
10.1073/pnas.95.12.6897
PubMed:
9618510
PubMed Central:
PMC22677

51. Phylogeny of hard- and soft-tick taxa (Acari: Ixodida) based on mitochondrial 16S rDNA sequences

Author:
Black, W.C. IV; Piesman, J.
Source:
Proceedings of the National Academy of Sciences of the United States of America 1994 v.91 no.21 pp. 10034-10038
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; Ixodidae; Argasidae; ribosomal DNA; ribosomal RNA; structural genes; nucleotide sequences; mitochondrial DNA; phylogeny; molecular conformation;     Show all 10 Subjects
Abstract:
... Ticks are parasitiform mites that are obligate hematophagous ectoparasites of amphibians, reptiles, birds, and mammals. A phylogeny for tick families, subfamilies, and genera has been described based on morphological characters, life histories, and host associations. To test the existing phylogeny, we sequenced approximately 460 bp from the 3' end of the mitochondrial 16S rRNA gene (rDNA) in 36 ha ...
DOI:
10.1073/pnas.91.21.10034
PubMed:
7937832
PubMed Central:
PMC44952

52. Gene elements that affect the longevity of rbcL sequence-containing transcripts in Chlamydomonas reinhardtii chloroplasts

Author:
Singh, M.; Boutanaev, A.; Zucchi, P.; Bogorad, L.
Source:
Proceedings of the National Academy of Sciences of the United States of America 2001 v.98 no.5 pp. 2289-2294
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; ribulose-bisphosphate carboxylase; messenger RNA; recombinant DNA; chloroplast DNA; mutation; reporter genes; ribonucleases; Chlamydomonas reinhardtii; degradation; genomics; molecular conformation; promoter regions; beta-glucuronidase; light; half life;     Show all 16 Subjects
Abstract:
... The chloroplast gene rbcL encodes the large subunit of the CO2-fixing enzyme ribulose-bisphosphate carboxylase. In previous work a target for photo-accelerated degradation of Chlamydomonas reinhardtii rbcL transcripts in vivo was found to lie within the first 63 nucleotides, and a sequence element required for increasing the longevity of transcripts of rbcL-reporter genes was found to occur betwee ...
DOI:
10.1073/pnas.041609798
PubMed:
11226232
PubMed Central:
PMC30131

53. Chrysanthemum chlorotic mottle viroid: unusual structural properties of a subgroup of self-cleaving viroids with hammerhead ribozymes

Author:
Navarro, B.; Flores, R.
Source:
Proceedings of the National Academy of Sciences of the United States of America 1997 v.94 no.21 pp. 11262-11267
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; Chrysanthemum chlorotic mottle viroid; chemical reactions; physicochemical properties; transcription (genetics); pathogenicity; Chrysanthemum morifolium; nucleotide sequences; lithium chloride; RNA; molecular conformation;     Show all 11 Subjects
Abstract:
... The causal agent of chrysanthemum chlorotic mottle (CChM) disease has been identified, cloned, and sequenced. It is a viroid RNA (CChMVd) of 398-399 nucleotides. In vitro transcripts with the complete CChMVd sequence were infectious and induced the typical symptoms of the CChM disease. CChMVd can form hammerhead structures in both polarity strands. Plus and minus monomeric CChMVd RNAs self-cleaved ...
DOI:
10.1073/pnas.94.21.11262
PubMed:
9326597
PubMed Central:
PMC23434

54. Plant mitochondrial nucleic acid sequences as a tool for phylogenetic analysis

Author:
Hiesel, R.; Haeseler, A. von.; Brennicke, A.
Source:
Proceedings of the National Academy of Sciences of the United States of America 1994 v.91 no.2 pp. 634-638
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; Polypodiopsida; structural genes; mitochondrial DNA; complementary DNA; phylogeny; Chlorophyta; cytochrome-c oxidase; Triticum aestivum; ferns and fern allies; molecular conformation; Gymnospermae; Bryopsida; introns; Oenothera;     Show all 15 Subjects
Abstract:
... To evaluate the potential of mitochondrial nucleic acid sequences as a phylogenetic tool, we have analyzed cytochrome oxidase subunit III (coxIII) coding sequences in representatives of the major groups of land plants. The phylogenetic tree derived from these mitochondrial sequences confirms the monophyletic origin of land plant mitochondria with the general order and descent of land plants deduce ...
DOI:
10.1073/pnas.91.2.634
PubMed:
7507251
PubMed Central:
PMC43003

55. Structure from function: screening structural models with functional data

Author:
Jin, L.; Cohen, F.E.; Wells, J.A.
Source:
Proceedings of the National Academy of Sciences of the United States of America 1994 v.91 no.1 pp. 113-117
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; humans; somatotropin; molecular conformation; prediction; epitopes; monoclonal antibodies; simulation models; algorithms; computer analysis; mutants; molecular models; binding sites; site-directed mutagenesis;     Show all 14 Subjects
Abstract:
... Structural constraints derived from different antibody epitopes on human growth hormone (hGH) were used to screen three-dimensional models of hGH that were generated by computer algorithms. Previously, alanine-scanning mutagenesis defined the residues that modulate binding to 21 different monoclonal antibodies to hGH. These functional epitopes were composed of 4-14 side chains whose alpha-carbons ...
DOI:
10.1073/pnas.91.1.113
PubMed:
7506411
PubMed Central:
PMC42896

56. Molecular and functional characterization of a novel low-affinity cation transporter (LCT1) in higher plants

Author:
Schachtman, D.P.; Kumar, R.; Schroeder, J.I.; Marsh, E.L.
Source:
Proceedings of the National Academy of Sciences of the United States of America 1997 v.94 no.20 pp. 11079-11084
ISSN:
0027-8424
Subject:
protein secondary structure,   etc   ; Triticum aestivum; complementary DNA; plant proteins; nucleotide sequences; amino acid sequences; molecular conformation; ion transport; sodium; rubidium; roots; leaves; mutants; Saccharomyces cerevisiae; plasma membrane; inorganic ions; calcium; genetic complementation;     Show all 18 Subjects
Abstract:
... The transport of cations across membranes in higher plants plays an essential role in many physiological processes including mineral nutrition, cell expansion, and the transduction of environmental signals. In higher plants the coordinated expression of transport mechanisms is essential for specialized cellular processes and for adaptation to variable environmental conditions. To understand the mo ...
DOI:
10.1073/pnas.94.20.11079
PubMed:
9380762
PubMed Central:
PMC23614