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Biochimica et biophysica acta
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7984-2016
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2016 v.1864 no.1
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- Author:
- Martijn Verdoes; Steven H.L. Verhelst
- Source:
- Biochimica et biophysica acta 2016 v.1864 no.1 pp. 130-142
- ISSN:
- 1570-9639
- Subject:
- animals; drugs; enzyme activity; image analysis; mass spectrometry; models; proteinases
- Abstract:
- ... Proteases are involved in a wide variety of biologically and medically important events. They are entangled in a complex network of processes that regulate their activity, which makes their study intriguing, but challenging. For comprehensive understanding of protease biology and effective drug discovery, it is therefore essential to study proteases in models that are close to their complex native ...
- DOI:
- 10.1016/j.bbapap.2015.04.029
- https://doi.org/10.1016/j.bbapap.2015.04.029
- Author:
- Mohan-Vivekanandan Poongavanam; Lydia Kisley; Katerina Kourentzi; Christy F. Landes; Richard C. Willson
- Source:
- Biochimica et biophysica acta 2016 v.1864 no.1 pp. 154-164
- ISSN:
- 1570-9639
- Subject:
- DNA; activation energy; dissociation; drugs; electrostatic interactions; enthalpy; entropy; enzymology; fluorescence; immunoglobulin E; ionic strength; kinetics; magnesium chloride; mutants; oligonucleotides; salt concentration; sodium chloride; spectroscopy; temperature
- Abstract:
- ... The IgE-binding DNA aptamer 17.4 is known to inhibit the interaction of IgE with the high-affinity IgE Fc receptor FcεRI. While this and other aptamers have been widely used and studied, there has been relatively little investigation of the kinetics and energetics of their interactions with their targets, by either single-molecule or ensemble methods.The dissociation kinetics of the D17.4/IgE comp ...
- DOI:
- 10.1016/j.bbapap.2015.08.008
- https://doi.org/10.1016/j.bbapap.2015.08.008
- Author:
- Alix Mignolet; Allison Derenne; Margarita Smolina; Bayden R. Wood; Erik Goormaghtigh
- Source:
- Biochimica et biophysica acta 2016 v.1864 no.1 pp. 85-101
- ISSN:
- 1570-9639
- Subject:
- Fourier transform infrared spectroscopy; antineoplastic agents; environmental factors; enzymes; enzymology; mechanism of action; neoplasm cells; neoplasms; proteins
- Abstract:
- ... Infrared spectroscopy has brought invaluable information about proteins and about the mechanism of action of enzymes. These achievements are difficult to transpose to living organisms as all biological molecules absorb in the mid infrared, with usually a high degree of overlap. Deciphering the contribution of each enzyme is therefore almost impossible. On the other hand, small changes in the infra ...
- DOI:
- 10.1016/j.bbapap.2015.08.010
- https://doi.org/10.1016/j.bbapap.2015.08.010
- Author:
- Sheng-Wei Yang; Hsiu-Chi Ting; Yi-Ting Lo; Ting-Yuan Wu; Hung-Wei Huang; Chia-Jung Yang; Jui-Fen Riva Chan; Min-Chieh Chuang; Yuan-Hao Howard Hsu
- Source:
- Biochimica et biophysica acta 2016 v.1864 no.1 pp. 42-51
- ISSN:
- 1570-9639
- Subject:
- active sites; bioactive properties; cardiovascular diseases; cell division; deuterium; enzyme activity; guanosine triphosphate; liquid chromatography; mass spectrometry; neoplasms; neurodegenerative diseases; solvents
- Abstract:
- ... Cdc42 regulates pathways related to cell division. Dysregulation of Cdc42 can lead to cancer, cardiovascular diseases and neurodegenerative diseases. GTP induced activation mechanism plays an important role in the activity and biological functions of Cdc42. P-loop, Switch I and Switch II are critical regions modulating the enzymatic activity of Cdc42. We applied amide hydrogen/deuterium exchange c ...
- DOI:
- 10.1016/j.bbapap.2015.10.007
- https://doi.org/10.1016/j.bbapap.2015.10.007
- Author:
- Nihed Ben Halima; Bassem Khemakhem; Imen Fendri; Hiroyuki Ogata; Patrick Baril; Chantal Pichon; Slim Abdelkafi
- Source:
- Biochimica et biophysica acta 2016 v.1864 no.1 pp. 52-61
- ISSN:
- 1570-9639
- Subject:
- sequence alignment; polyacrylamide gel electrophoresis; wheat; catalytic activity; liquid chromatography; X-radiation; barley; Hordeum vulgare; open reading frames; amino acids; Triticum aestivum; active sites; molecular weight; beta-amylase; databases; complementary DNA; Secale cereale; amino acid sequences; rye; proteomics; enzyme activity; proteins; seed extracts; oats; expressed sequence tags; tandem mass spectrometry; Avena sativa
- Abstract:
- ... Oat (Avena sativa L.) seed extracts exhibited a high degree of catalytic activity including amylase activities. Proteins in the oat seed extracts were optimized for their amylolytic activities. Oat extract with amylolytic activity was separated by SDS-PAGE and a major protein band with an apparent molecular mass of 53kDa was subjected to tryptic digestion. The generated amino acid sequences were a ...
- DOI:
- 10.1016/j.bbapap.2015.10.001
- https://doi.org/10.1016/j.bbapap.2015.10.001
- Author:
- Yin-Ming Kuo; Ryan A. Henry; Andrew J. Andrews
- Source:
- Biochimica et biophysica acta 2016 v.1864 no.1 pp. 70-76
- ISSN:
- 1570-9639
- Subject:
- enzyme activity; enzymes; prediction
- Abstract:
- ... Multiple substrate enzymes present a particular challenge when it comes to understanding their activity in a complex system. Although a single target may be easy to model, it does not always present an accurate representation of what that enzyme will do in the presence of multiple substrates simultaneously. Therefore, there is a need to find better ways to both study these enzymes in complicated s ...
- DOI:
- 10.1016/j.bbapap.2015.08.011
- PubMed:
- 26321598
- PubMed Central:
- PMC4924809
- https://doi.org/10.1016/j.bbapap.2015.08.011
- Author:
- Sigurbjörg Rutardottir; Elena Karnaukhova; Chanin Nantasenamat; Napat Songtawee; Virapong Prachayasittikul; Mohsen Rajabi; Lena Wester Rosenlöf; Abdu I. Alayash; Bo Åkerström
- Source:
- Biochimica et biophysica acta 2016 v.1864 no.1 pp. 29-41
- ISSN:
- 1570-9639
- Subject:
- absorbance; binding sites; circular dichroism spectroscopy; crystal structure; cysteine; electrophoresis; fluorescence; gel chromatography; heme; heme iron; histidine; lysine; models; serine; site-directed mutagenesis; threonine; tryptophan
- Abstract:
- ... α1-Microglobulin (A1M) is a reductase and radical scavenger involved in physiological protection against oxidative damage. These functions were previously shown to be dependent upon cysteinyl-, C34, and lysyl side-chains, K(92, 118,130). A1M binds heme and the crystal structure suggests that C34 and H123 participate in a heme binding site. We have investigated the involvement of these five residue ...
- DOI:
- 10.1016/j.bbapap.2015.10.002
- https://doi.org/10.1016/j.bbapap.2015.10.002
- Author:
- Casey L. Kohnhorst; Danielle L. Schmitt; Anand Sundaram; Songon An
- Source:
- Biochimica et biophysica acta 2016 v.1864 no.1 pp. 77-84
- ISSN:
- 1570-9639
- Subject:
- enzymology; fluorescence; intracellular space; microscopy; protein-protein interactions; proteins; space and time
- Abstract:
- ... A cell is a highly organized, dynamic, and intricate biological entity orchestrated by a myriad of proteins and their self-assemblies. Because a protein's actions depend on its coordination in both space and time, our curiosity about protein functions has extended from the test tube into the intracellular space of the cell. Accordingly, modern technological developments and advances in enzymology ...
- DOI:
- 10.1016/j.bbapap.2015.05.014
- PubMed:
- 26025769
- PubMed Central:
- PMC5679394
- https://doi.org/10.1016/j.bbapap.2015.05.014
- Author:
- E.F. Peloso; L. Dias; R.M.L. Queiroz; A.F.P. Paes Leme; C.N. Pereira; C.M. Carnielli; C.C. Werneck; M.V. Sousa; C.A.O. Ricart; F.R. Gadelha
- Source:
- Biochimica et biophysica acta 2016 v.1864 no.1 pp. 1-10
- ISSN:
- 1570-9639
- Subject:
- Trypanosoma cruzi; antioxidant activity; antioxidants; coprecipitation; homeostasis; mass spectrometry; mechanism of action; metabolism; mitochondria; oxidative stress; peroxiredoxin; proteins; stress response; thiols
- Abstract:
- ... Trypanosoma cruzi depends on the effectiveness of redox metabolism to survive and ensure infection in the host. Homeostasis of redox metabolism in T. cruzi is achieved by the actions of several proteins that differ in many aspects from host proteins. Although extensive research has been performed examining hydroperoxide cytosolic antioxidant defense centered on trypanothione, the mechanisms of mit ...
- DOI:
- 10.1016/j.bbapap.2015.10.005
- https://doi.org/10.1016/j.bbapap.2015.10.005
- Author:
- Jung-Suk Choi; Anthony J. Berdis
- Source:
- Biochimica et biophysica acta 2016 v.1864 no.1 pp. 165-176
- ISSN:
- 1570-9639
- Subject:
- DNA; DNA damage; autoimmune diseases; biophotonics; enzymology; homeostasis; metabolism; neoplasms; nucleosides; radiolabeling; transporters
- Abstract:
- ... Nucleosides and their corresponding mono-, di-, and triphosphates play important roles in maintaining cellular homeostasis. In addition, perturbations in this homeostasis can result in dysfunctional cellular processes that cause pathological conditions such as cancer and autoimmune diseases. This review article discusses contemporary research areas applying nucleoside analogs to probe the mechanis ...
- DOI:
- 10.1016/j.bbapap.2015.05.010
- https://doi.org/10.1016/j.bbapap.2015.05.010
- Author:
- Graham R. Moran
- Source:
- Biochimica et biophysica acta 2016 v.1864 no.1 pp. 177-186
- ISSN:
- 1570-9639
- Subject:
- autoxidation; blood pressure; catalytic activity; catecholamines; electrons; enzyme substrates; heart; humans; hydrogen peroxide; kidneys; metabolism; physiological response; renalase; seeds
- Abstract:
- ... Ten years after the initial identification of human renalase the first genuinely catalytic substrates have been identified. Throughout the prior decade a consensus belief that renalase is produced predominantly by the kidney and catalytically oxidizes catecholamines in order to lower blood pressure and slow the heart has prevailed. This belief was, however, based on fundamentally flawed scientific ...
- DOI:
- 10.1016/j.bbapap.2015.04.010
- https://doi.org/10.1016/j.bbapap.2015.04.010
- Author:
- Bao Quoc Tran; David R. Goodlett; Young Ah Goo
- Source:
- Biochimica et biophysica acta 2016 v.1864 no.1 pp. 123-129
- ISSN:
- 1570-9639
- Subject:
- amino acids; bioinformatics; chemical analysis; cross-linking reagents; crosslinking; enzymology; mass spectrometry; models; peptides; protein binding; protein-protein interactions; stoichiometry
- Abstract:
- ... For the analysis of protein-protein interactions and protein conformations, cross-linking coupled with mass spectrometry (CXMS) has become an essential tool in recent years. A variety of cross-linking reagents are used to covalently link interacting amino acids to identify protein-binding partners. The spatial proximity of cross-linked amino acid residues is used to elucidate structural models of ...
- DOI:
- 10.1016/j.bbapap.2015.05.015
- https://doi.org/10.1016/j.bbapap.2015.05.015
- Author:
- Li-Zhi Hu; Wei-Ping Zhang; Mao-Tian Zhou; Qiang-Qiang Han; Xiao-Li Gao; Hao-Long Zeng; Lin Guo
- Source:
- Biochimica et biophysica acta 2016 v.1864 no.1 pp. 20-28
- ISSN:
- 1570-9639
- Subject:
- Salmonella; homeostasis; magnesium; mass spectrometry; monitoring; proteins; proteomics
- Abstract:
- ... SRM (selected reaction monitoring), a tandem mass spectrometry-based method characterized by high repeatability and accuracy, is an effective tool for the quantification of predetermined proteins. In this study, we built a time-scheduled dimethyl-SRM method that can provide the precise relative quantification of 92 proteins in one run. By applying this method to the Salmonella PhoP/PhoQ two-compon ...
- DOI:
- 10.1016/j.bbapap.2015.10.003
- https://doi.org/10.1016/j.bbapap.2015.10.003
- Author:
- Irene Lee; Anthony J. Berdis
- Source:
- Biochimica et biophysica acta 2016 v.1864 no.1 pp. 65-69
- ISSN:
- 1570-9639
- Subject:
- cell biology; enzymes; enzymology; image analysis; instrumentation; physicochemical properties; protein structure; proteins
- Abstract:
- ... Historically, the study of proteins has relied heavily on characterizing the activity of a single purified protein isolated from other cellular components. This classic approach allowed scientists to unambiguously define the intrinsic kinetic and chemical properties of that protein. The ultimate hope was to extrapolate this information toward understanding how the enzyme or receptor behaves within ...
- DOI:
- 10.1016/j.bbapap.2015.07.011
- https://doi.org/10.1016/j.bbapap.2015.07.011
- Author:
- Ankita Singh; Rahul Kaushik; Avinash Mishra; Asheesh Shanker; B. Jayaram
- Source:
- Biochimica et biophysica acta 2016 v.1864 no.1 pp. 11-19
- ISSN:
- 1570-9639
- Subject:
- prediction; protein tertiary structure; proteins
- Abstract:
- ... Quality assessment of predicted model structures of proteins is as important as the protein tertiary structure prediction. A highly efficient quality assessment of predicted model structures directs further research on function. Here we present a new server ProTSAV, capable of evaluating predicted model structures based on some popular online servers and standalone tools. ProTSAV furnishes the use ...
- DOI:
- 10.1016/j.bbapap.2015.10.004
- https://doi.org/10.1016/j.bbapap.2015.10.004
- Author:
- Libo Wang; Ying Liu; Lijun Wu; Xue-Long Sun
- Source:
- Biochimica et biophysica acta 2016 v.1864 no.1 pp. 143-153
- ISSN:
- 1570-9639
- Subject:
- aromatic compounds; cell adhesion; cytidine; drugs; enzyme inhibitors; flavonoids; glycoconjugates; immune response; inflammation; lipids; lithocholic acid; metastasis; neoplasm cells; neoplasms; oligosaccharides; proteins; sialic acids; therapeutics
- Abstract:
- ... Sialic acids, existing as terminal sugars of glycoconjugates, play important roles in various physiological and pathological processes, such as cell–cell adhesion, immune defense, tumor cell metastasis, and inflammation. Sialyltransferases (STs) catalyze the transfer of sialic acid residues to non-reducing oligosaccharide chains of proteins and lipids, using cytidine monophosphate N-acetylneuramin ...
- DOI:
- 10.1016/j.bbapap.2015.07.007
- https://doi.org/10.1016/j.bbapap.2015.07.007
- Author:
- Zhu Liu; Zhou Gong; Xu Dong; Chun Tang
- Source:
- Biochimica et biophysica acta 2016 v.1864 no.1 pp. 115-122
- ISSN:
- 1570-9639
- Subject:
- nuclear magnetic resonance spectroscopy; protein-protein interactions; proteins
- Abstract:
- ... Proteins interact with each other to establish their identities in cell. The affinities for the interactions span more than ten orders of magnitude, and KD values in μM–mM regimen are considered transient and are important in cell signaling. Solution NMR including diamagnetic and paramagnetic techniques has enabled atomic-resolution depictions of transient protein–protein interactions. Diamagnetic ...
- DOI:
- 10.1016/j.bbapap.2015.04.009
- https://doi.org/10.1016/j.bbapap.2015.04.009
- Author:
- Michael Assfalg; Laura Ragona; Katiuscia Pagano; Mariapina D'Onofrio; Serena Zanzoni; Simona Tomaselli; Henriette Molinari
- Source:
- Biochimica et biophysica acta 2016 v.1864 no.1 pp. 102-114
- ISSN:
- 1570-9639
- Subject:
- carbon; gold; hydrodynamics; lipids; medicine; nanoparticles; nuclear magnetic resonance spectroscopy; polymers; proteins; silica; silver; surveys
- Abstract:
- ... The rapid development of novel nanoscale materials for applications in biomedicine urges an improved characterization of the nanobio interfaces. Nanoparticles exhibit unique structures and properties, often different from the corresponding bulk materials, and the nature of their interactions with biological systems remains poorly characterized. Solution NMR spectroscopy is a mature technique for t ...
- DOI:
- 10.1016/j.bbapap.2015.04.024
- https://doi.org/10.1016/j.bbapap.2015.04.024