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1. Versatile N-Methylaminooxy-Functionalized Polypeptides for Preparation of Neoglycoconjugates

Author:
Wollenberg, Alexander L.; Perlin, Pesach; Deming, Timothy J.
Source:
Biomacromolecules 2019 v.20 no.4 pp. 1756-1764
ISSN:
1526-4602
Subject:
polypeptides,   etc   ; glycoproteins; hydrophobicity; moieties; pH;     Show all 5 Subjects
Abstract:
... The preparation and characterization of a new set of well-defined polypeptides containing N-methylaminooxy side-chain functionality is described. These functional groups enabled the direct coupling of polypeptides with a variety of unmodified reducing saccharides in water to give neoglycopolypeptides in high yields. The use of different polypeptide scaffolds resulted in neoglycoconjugates with tun ...
DOI:
10.1021/acs.biomac.9b00138

2. Orientational and Folding Thermodynamics via Electric Dipole Moment Restraining

Author:
Garate, Jose Antonio; Bernardin, Alejandro; Escalona, Yerko; Yanez, Carlos; English, Niall J.; Perez-Acle, Tomas
Source:
TheJournal of physical chemistry 2019 v.123 no.12 pp. 2599-2608
ISSN:
1520-5207
Subject:
polypeptides,   etc   ; electric potential difference; thermodynamics;     Show all 3 Subjects
Abstract:
... The projection of molecular processes onto a small set of relevant descriptors, the so-called reaction coordinates or collective variables (CVs), is a technique nowadays routinely employed by the biomolecular simulation community. In this work, we implemented two CVs to manipulate the orientation (i.e., angle) (μ⃗ₐ) and magnitude (|μ⃗|) of the electric dipole moment. In doing so, we studied the th ...
DOI:
10.1021/acs.jpcb.8b09374

3. Homogenous deposition of matrix–analyte cocrystals on gold-nanobowl arrays for improving MALDI-MS signal reproducibility

Author:
Li, Weiwei; Khan, Mashooq; Li, Haifang; Lin, Ling; Mao, Sifeng; Lin, Jin-Ming
Source:
Chemical communications 2019 v.55 no.15 pp. 2166-2169
ISSN:
1364-548X
Subject:
polypeptides,   etc   ; chemical compounds; ionization; oligonucleotides; quantitative analysis;     Show all 5 Subjects
Abstract:
... The non-uniform deposition of matrix–analyte cocrystals and poor ionization are major obstacles in quantitative analysis through MALDI-MS. An Au-nanobowl array was prepared and applied to overcome these limitations, which enabled the quantitative detection of oligonucleotides and polypeptides. ...
DOI:
10.1039/c8cc09945f

4. Misfolding of a Human Islet Amyloid Polypeptide at the Lipid Membrane Populates through β-Sheet Conformers without Involving α-Helical Intermediates

Author:
Tan, Junjun; Zhang, Jiahui; Luo, Yi; Ye, Shuji
Source:
Journal of the American Chemical Society 2019 v.141 no.5 pp. 1941-1948
ISSN:
1520-5126
Subject:
polypeptides,   etc   ; amyloid; humans; lipid bilayers; lipids; spectroscopy;     Show all 6 Subjects
Abstract:
... Amyloid formation has been implicated in many fatal diseases, but its mechanism remains to be clarified due to a lack of effective methods that can capture the transient intermediates. Here, we experimentally demonstrate that sum frequency generation vibrational spectroscopy can unambiguously discriminate the intermediates during amyloid formation at the lipid membrane in situ and in real time by ...
DOI:
10.1021/jacs.8b08537

5. Clustered complementary amino acid pairing (CCAAP) for protein–protein interaction

Author:
Baek, Christina Kyung Eun; Baek, Chang-Ho
Source:
Biotechnology letters 2019 v.41 no.1 pp. 79-90
ISSN:
0141-5492
Subject:
polypeptides,   etc   ; amino acids; protein-protein interactions; stereochemistry;     Show all 4 Subjects
Abstract:
... OBJECTIVES: Designing a polypeptide sequence to interact with a preselected target polypeptide sequence of a protein has long been of interest, yet remains an elusive goal. RESULTS: Here, we propose a novel concept named “Clustered Complementary Amino Acid Pairing (CCAAP),” which plays an essential role in protein–protein interaction (PPI). Complementary amino acid pairing (CAAP) is a pairing betw ...
DOI:
10.1007/s10529-018-2616-2

6. Investigating the Effect of Chain Connectivity on the Folding of a Beta-Sheet Protein On and Off the Ribosome

Author:
Marsden, Andrew P.; Hollins, Jeffrey J.; O’Neill, Charles; Ryzhov, Pavel; Higson, Sally; Mendonça, Carolina A.T.F.; Kwan, Tristan O.; Kwa, Lee Gyan; Steward, Annette; Clarke, Jane
Source:
Journal of molecular biology 2018 v.430 no.24 pp. 5207-5216
ISSN:
0022-2836
Subject:
polypeptides,   etc   ; protein folding; ribosomes;     Show all 3 Subjects
Abstract:
... Determining the relationship between protein folding pathways on and off the ribosome remains an important area of investigation in biology. Studies on isolated domains have shown that alteration of the separation of residues in a polypeptide chain, while maintaining their spatial contacts, may affect protein stability and folding pathway. Due to the vectorial emergence of the polypeptide chain fr ...
DOI:
10.1016/j.jmb.2018.10.011

7. Construction of Challenging Proline–Proline Junctions via Diselenide–Selenoester Ligation Chemistry

Author:
Sayers, Jessica; Karpati, Phillip M. T.; Mitchell, Nicholas J.; Goldys, Anna M.; Kwong, Stephen M.; Firth, Neville; Chan, Bun; Payne, Richard J.
Source:
Journal of the American Chemical Society 2018 v.140 no.41 pp. 13327-13334
ISSN:
1520-5126
Subject:
polypeptides,   etc   ; moieties; proline; proteins;     Show all 4 Subjects
Abstract:
... Polyproline sequences are highly abundant in prokaryotic and eukaryotic proteins, where they serve as key components of secondary structure. To date, construction of the proline–proline motif has not been possible owing to steric congestion at the ligation junction, together with an n → π* electronic interaction that reduces the reactivity of acylated proline residues at the C-terminus of peptides ...
DOI:
10.1021/jacs.8b07877

8. Self-Assembly of α-Helical Polypeptides into Microscopic and Enantiomorphic Spirals

Author:
Vacogne, Charlotte D.; Wei, Chunxiang; Tauer, Klaus; Schlaad, Helmut
Source:
Journal of the American Chemical Society 2018 v.140 no.36 pp. 11387-11394
ISSN:
1520-5126
Subject:
polypeptides,   etc   ; emulsifying; optical isomerism;     Show all 3 Subjects
Abstract:
... Helical structures are ubiquitous in biological materials and often serve a structural purpose. Bioinspired helical materials can be challenging to synthesize and rarely reach the degree of hierarchy of their natural counterparts. Here we report the first example of particles synthesized by direct emulsification of polypeptides found to display spiral morphologies in the dry state. The polypeptide ...
DOI:
10.1021/jacs.8b06503

9. Translocation of non-interacting heteropolymer protein chains in terms of single helical propensity and size

Author:
Olivares-Quiroz, L.; Vélez-Pérez, José Antonio
Source:
Biochimica et biophysica acta 2019 v.1867 no.6 pp. 565-574
ISSN:
1570-9639
Subject:
polypeptides,   etc   ; Gibbs free energy; amino acids; energy; entropy; proteins;     Show all 6 Subjects
Abstract:
... In this work we present an analytical framework to calculate the average translocation time τ required for an ideal proteinogenic polypeptide chain to cross over a small pore on a membrane. Translocation is considered to proceed as a chain of non-interacting amino acid residues of sequence {Xj} diffuses through the pore against an energy barrier Δℱ, set by chain entropy and unfolding-folding energ ...
DOI:
10.1016/j.bbapap.2019.03.003

10. Selective Hsp70-Dependent Docking of Hsp104 to Protein Aggregates Protects the Cell from the Toxicity of the Disaggregase

Author:
Chamera, Tomasz; Kłosowska, Agnieszka; Janta, Anna; Wyszkowski, Hubert; Obuchowski, Igor; Gumowski, Krzysztof; Liberek, Krzysztof
Source:
Journal of molecular biology 2019 v.431 no.11 pp. 2180-2196
ISSN:
0022-2836
Subject:
polypeptides,   etc   ; adenosinetriphosphatase; phenylalanine; protein aggregates; substrate specificity; toxicity; yeasts;     Show all 7 Subjects
Abstract:
... Hsp104 is a yeast chaperone that rescues misfolded proteins from aggregates associated with proteotoxic stress and aging. Hsp104 consists of N-terminal domain, regulatory M-domain and two ATPase domains, assembled into a spiral-shaped hexamer. Protein disaggregation involves polypeptide extraction from an aggregate and its translocation through the central channel. This process relies on Hsp104 co ...
DOI:
10.1016/j.jmb.2019.04.014

11. A minimum set of stable blocks for rational design of polypeptide chains

Author:
Nekrasov, Alexei N.; Alekseeva, Ludmila G.; Pogosyan, Rudolf А.; Dolgikh, Dmitry A.; Kirpichnikov, M.P.; de Brevern, Alexandre G.; Anashkina, Anastasia A.
Source:
Biochimie 2019 v.160 pp. 88-92
ISSN:
0300-9084
Subject:
polypeptides,   etc   ; alanine; moieties; molecular dynamics; protein secondary structure; topology;     Show all 6 Subjects
Abstract:
... The aim of this work was to find a minimal set of structurally stable pentapeptides, which allows forming a polypeptide chain of a required 3D structure. To search for factors that ensure structural stability of the pentapeptide, we generated peptide sequences with no more than three functional groups, based on the alanine pentapeptide AAAAA. We analyzed 44,860 structures of peptides by the molecu ...
DOI:
10.1016/j.biochi.2019.02.006

12. Pre-structured hydrophobic peptide β-strands: A universal amyloid trap?

Author:
Sivanesam, Kalkena; Andersen, Niels
Source:
Archives of biochemistry and biophysics 2019 v.664 pp. 51-61
ISSN:
0003-9861
Subject:
polypeptides,   etc   ; amyloid; cross reaction; humans; hydrophobicity; sequence homology;     Show all 6 Subjects
Abstract:
... Amyloid fibril formation has long been studied because of the variety of proteins that are capable of adopting this structure despite sharing little sequence homology. This makes amyloid fibrils a challenging focus for inhibition studies because the peptides and proteins that form amyloid fibrils cannot be targeted based on a sequence motif. Most peptide inhibitors that target specific amyloidogen ...
DOI:
10.1016/j.abb.2019.01.032

13. In silico design of mimosine containing peptides as new efficient chelators of aluminum

Author:
Mujika, J. I.; Dalla Torre, G.; Lachowicz, J. I.; Lopez, X.
Source:
RSC advances 2019 v.9 no.14 pp. 7688-7697
ISSN:
2046-2069
Subject:
polypeptides,   etc   ; aluminum; cell membranes; chelating agents; ligands; mimosine; therapeutics; toxicity;     Show all 8 Subjects
Abstract:
... The design of new and efficient chelators that can remove aluminium(iii), a metal with increasing recognition as a potential toxic agent, from biological systems is an area of high therapeutic relevance. In the present paper, we present an extensive computational study of a new promising type of these chelators based on mimosine containing peptides. The reason to choose mimosine is that the sidech ...
DOI:
10.1039/c8ra10139f

14. Globular protein backbone conformational disorder in crystal structures

Author:
Carugo, Oliviero
Source:
Amino acids 2019 v.51 no.3 pp. 475-481
ISSN:
0939-4451
Subject:
polypeptides,   etc   ; amino acids; crystal structure; protein structure; proteins; thermodynamics;     Show all 6 Subjects
Abstract:
... Proteins are not static molecules but dynamic entities able to modify their structure for several reasons, from the necessity to recognize partners to the regulation of their thermodynamic stability. Conformational disorder is frequent in protein structures and atoms can have, in protein crystal structures, two or more alternative, equilibrium positions close to each other. Here, a set of protein ...
DOI:
10.1007/s00726-018-2683-7

15. Glycosaminoglycans Induce Amyloid Self-Assembly of a Peptide Hormone by Concerted Secondary and Quaternary Conformational Transitions

Author:
Sebastiao, Mathew; Quittot, Noe; Marcotte, Isabelle; Bourgault, Steve
Source:
Biochemistry 2019 v.58 no.9 pp. 1214-1225
ISSN:
1520-4995
Subject:
polypeptides,   etc   ; RNA; amyloid; anions; heparan sulfate; particulates; peptide hormones;     Show all 7 Subjects
Abstract:
... Amyloids are polypeptide supramolecular assemblies that have been historically associated with numerous pathologies. Nonetheless, recent studies have identified many amyloid structures that accomplish vital physiological functions. Interestingly, amyloid fibrils, either pathological or functional, have been reported to be consistently associated with other biomolecules such as RNA and glycosaminog ...
DOI:
10.1021/acs.biochem.8b01206

16. Role of Diffusion in Unfolding and Translocation of Multidomain Titin I27 Substrates by a Clp ATPase Nanomachine

Author:
Javidialesaadi, Abdolreza; Flournoy, Shanice M.; Stan, George
Source:
TheJournal of physical chemistry 2019 v.123 no.12 pp. 2623-2635
ISSN:
1520-5207
Subject:
polypeptides,   etc   ; adenosinetriphosphatase; amino acid sequences; forces; geometry; optical traps; proteins;     Show all 7 Subjects
Abstract:
... Degradation of multidomain substrate proteins (SPs) by AAA+ nanomachines takes place processively from the tagged terminal. Ring-shaped ATPase components, such as ClpY, apply repetitive mechanical forces to effect domain unfolding and translocation of polypeptide segments through a narrow central channel. We study these mechanisms through atomistic Langevin dynamics simulations of C-terminal-tagge ...
DOI:
10.1021/acs.jpcb.8b10282

17. Regulation of Human Hsc70 ATPase and Chaperone Activities by Apg2: Role of the Acidic Subdomain

Author:
Cabrera, Yovana; Dublang, Leire; Fernández-Higuero, José Angel; Albesa-Jové, David; Lucas, Maria; Viguera, Ana Rosa; Guerin, Marcelo E.; Vilar, Jose M.G.; Muga, Arturo; Moro, Fernando
Source:
Journal of molecular biology 2019 v.431 no.2 pp. 444-461
ISSN:
0022-2836
Subject:
polypeptides,   etc   ; Animalia; adenosinetriphosphatase; dissociation; humans; hydrolysis; mutants; protein aggregates;     Show all 8 Subjects
Abstract:
... Protein aggregate reactivation in metazoans is accomplished by the combined activity of Hsp70, Hsp40 and Hsp110 chaperones. Hsp110s support the refolding of aggregated polypeptides acting as specialized nucleotide exchange factors of Hsp70. We have studied how Apg2, one of the three human Hsp110s, regulates the activity of Hsc70 (HspA8), the constitutive Hsp70 in our cells. Apg2 shows a biphasic b ...
DOI:
10.1016/j.jmb.2018.11.026

18. Inverse Correlation between Amyloid Stiffness and Size

Author:
Nassar, Roy; Wong, Eric; Gsponer, Jörg; Lamour, Guillaume
Source:
Journal of the American Chemical Society 2018 v.141 no.1 pp. 58-61
ISSN:
1520-5126
Subject:
polypeptides,   etc   ; amyloid; hydrogen bonding; topology;     Show all 4 Subjects
Abstract:
... We reveal that the axial stiffness of amyloid fibrils is inversely correlated with their cross-sectional area. Because amyloid fibrils’ stiffness is determined by hydrogen bond (H-bond) density with a linear correlation, our finding implies that amyloid fibrils with larger radial sizes are generally softer and have lower density H-bond networks. In silico calculations show that the stiffness–size ...
DOI:
10.1021/jacs.8b10142

19. Correction: IR820 covalently linked with self-assembled polypeptide for photothermal therapy applications in cancer

Author:
Huang, Kaizong; Gao, Mengyue; Fan, Lin; Lai, Yueyang; Fan, Hongwei; Hua, Zichun
Source:
Biomaterials science 2018 v.6 no.12 pp. 3410
ISSN:
2047-4849
Subject:
polypeptides,   etc   ; chemical bonding; neoplasms; photothermotherapy;     Show all 4 Subjects
Abstract:
... Correction for ‘IR820 covalently linked with self-assembled polypeptide for photothermal therapy applications in cancer’ by Kaizong Huang et al., Biomater. Sci., 2018, 6, 2925–2931. ...
DOI:
10.1039/c8bm90057d

20. Computational Investigation of the Effect of Backbone Chiral Inversions on Polypeptide Structure B

Author:
Zerze, Gül H.; Khan, Mohammad Navaid; Stillinger, Frank H.; Debenedetti, Pablo G.
Source:
The Journal of physical chemistry 2018 v.122 no.24 pp. 6357-6363
ISSN:
1520-5207
Subject:
polypeptides,   etc   ; optical isomerism; physical chemistry;     Show all 3 Subjects
Abstract:
... Studying a set of helix-folding polyalanine peptides with systematically inserted chiral inversions in explicit water, we investigate quantitatively the effect of chiral perturbations on the structural ensembles of the peptides, thereby assessing the extent to which the backbone structure is able to fold in the presence of systematic heterochiral perturbations. Starting from the homochiral l-Ala₂₀ ...
DOI:
10.1021/acs.jpcb.8b03157