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Planning combinatorial disulfide cross-links for protein fold determination
2011
BMC Bioinformatics
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Results: This paper presents an integrated computational-experimental method to determine the fold of a target protein by probing it with a set of planned disulfide cross-links. ...
In a second stage, we determine a set of residue-level cross-links to probe the selected SSE pairs. ...
Once we have identified a subset of SSE pairs that are most informative for fold determination, we plan disulfide cross-links to evaluate these SSE pairs; see the right panel of Fig. 1 . ...
doi:10.1186/1471-2105-12-s12-s5
pmid:22168447
pmcid:PMC3247086
fatcat:fzwovqbrp5b2nl4qpw4q5vkwr4
Probabilistic cross-link analysis and experiment planning for high-throughput elucidation of protein structure
2009
Protein Science
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We also describe an experiment plan for the bacteriophage Tfa chaperone protein in which we plan dicysteine mutants for discriminating threading models by disulfide formation. ...
One such technique uses cross-linking (chemical or by cysteine oxidation) to confirm or select among proposed structural models (e.g., from fold recognition, ab initio prediction, or docking) by testing ...
Thanks also to Shobha Potluri and Aly Azeem Khan, Department of Computer Science, Purdue University, for help with the test cases and cross-linking distance analysis. ...
doi:10.1110/ps.04846604
pmid:15557270
pmcid:PMC2287312
fatcat:5tw3gr6bnvgctbceru3lbuhgu4
Oxidation of an Exposed Methionine Instigates the Aggregation of Glyceraldehyde-3-phosphate Dehydrogenase
2014
Journal of Biological Chemistry
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Despite the fact that disulfide cross-linking is a prominent feature of GAPDH aggregation, our data show that it is not a primary rate-determining step. ...
GAPDH normally exists in a soluble form; however, following necrosis, GAPDH and numerous other intracellular proteins convert into an insoluble disulfidecross-linked state via the process of "nucleocytoplasmic ...
whereby its oxidation is a primary event permissive for the subsequent misfolding, aggregation, and disulfide cross-linking of GAPDH. ...
doi:10.1074/jbc.m114.570275
pmid:25086035
pmcid:PMC4175333
fatcat:xilxdewki5cmbmvzkc2xw72vpa
Prm1 Functions as a Disulfide-linked Complex in Yeast Mating
2009
Journal of Biological Chemistry
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Cys 120 in loop 1 and Cys 545 in loop 2 form disulfide cross-links in the Prm1 homodimer and are required for fusion activity. ...
HA-Prm1 migrates at twice its expected molecular weight on nonreducing SDS-PAGE gels and coprecipitates with Prm1-TAP, indicating that Prm1 is a disulfide-linked homodimer. ...
Intracellular Localization of the Cys to Ser Mutant Prm1 Proteins-In yeast, as in mammalian cells, disulfide-bonded proteins must be properly folded and cross-linked before they can exit the ER (16) . ...
doi:10.1074/jbc.m109.068874
pmid:19933274
pmcid:PMC2807284
fatcat:abzveotprjbcdav22cgmiavsku
Defining the Disulfide Bonds of Insulin-like Growth Factor-binding Protein-5 by Tandem Mass Spectrometry with Electron Transfer Dissociation and Collision-induced Dissociation
2011
Journal of Biological Chemistry
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Only 2 of 9 putative disulfide bonds have been mapped for IGFBP-5. ...
of ab initio molecular modeling to characterize unknown disulfide linkages in proteins. ...
Acknowledgments-We thank Tony Capps, Debra McMillen, and John Klimek for experimental and technical advice, and the assistance of the OHSU Shared Proteomics Resource. ...
doi:10.1074/jbc.m111.285528
pmid:22117064
pmcid:PMC3256881
fatcat:wohzeyyfjngtxhaod53iuufhti
In vitro Evolution of Catalytic Antibodies and Other Proteins via Combinatorial Libraries
[chapter]
2005
Catalytic Antibodies
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Yoram Reiter of the Technion for helpful advice and comments on this manuscript. ...
The uncoupled, free cysteine was planned to form an S-S bond with an active disulfide acceptor, which was immobilized on microtiter plates [44] . ...
via Combinatorial Libraries
In vitro Evolution of Catalytic Antibodies and Other Proteins via Combinatorial Libraries ...
doi:10.1002/3527603662.ch9
fatcat:ukdbrmmu4vbadcol3tsdhxjmii
Engineering stable carbonic anhydrases for CO2 capture: a critical review
2021
Protein Engineering Design & Selection
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Targeted inhibition of misregulated protein–protein interactions (PPIs) has been a promising area of investigation in drug discovery and development for human diseases. ...
The strategies described here can be explored for other protein–protein interactions and aid in designing new libraries or improving on previous libraries. ...
Energetically, an overall loss of entropy favors the stabilization of the folded state, and disulfide bridges that covalently link two regions of the proteins are expected to decrease the entropy and thereby ...
doi:10.1093/protein/gzab021
pmid:34427656
fatcat:zynkqrkbz5guxnrtvijg3lb64y
From atoms to systems: a cross-disciplinary approach to complement-mediated functions*1
2004
Molecular Immunology
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Our laboratory has adopted such a cross-disciplinary approach in elucidating key aspects of complement functions and determining the role of several complement proteins in both inflammatory and developmental ...
The unidirectional study of single molecules and pathways is being replaced by a combinatorial and cross-disciplinary platform that investigates interactive biological systems and dynamic networks. ...
Acknowledgements We would like to thank all present and past members of our laboratories, as well as our collaborators from other institutions, for their contribution to the various research projects discussed ...
doi:10.1016/s0161-5890(04)00078-1
fatcat:srfjy25vebaq5a34wwp7u3zrt4
From atoms to systems: a cross-disciplinary approach to complement-mediated functions*1
2004
Molecular Immunology
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Our laboratory has adopted such a cross-disciplinary approach in elucidating key aspects of complement functions and determining the role of several complement proteins in both inflammatory and developmental ...
The unidirectional study of single molecules and pathways is being replaced by a combinatorial and cross-disciplinary platform that investigates interactive biological systems and dynamic networks. ...
Acknowledgements We would like to thank all present and past members of our laboratories, as well as our collaborators from other institutions, for their contribution to the various research projects discussed ...
doi:10.1016/j.molimm.2004.03.016
pmid:15159061
fatcat:q2lqshnrevfblgsstmqcgaktm4
An automated method for modeling proteins on known templates using distance geometry
2008
Protein Science
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The resulting geometry of the nonhomologous disulfide in the model structure for murine IL-4 is consistent with standard disulfide geometry. ...
We present an automated method incorporated into a software package, FOLDER, to fold a protein sequence on a given three-dimensional (3D) template. ...
Disulfide cross-links in the three structures are shown in CPK. Full atomic structure in red is shown for one simulated structure. ...
doi:10.1002/pro.5560020216
pmid:8443604
pmcid:PMC2142344
fatcat:gyijnlrxr5glxhhpfspu3kbba4
Conformational interconversion in compstatin probed with molecular dynamics simulations
2003
Proteins: Structure, Function, and Bioinformatics
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Proteins 2003;52:130 -141. ...
In our effort to understand the structural and dynamic characteristics of compstatin that form the basis for rational and combinatorial optimization of structure and activity, we performed 1-ns molecular ...
Richard Henchman for critical reading of the manuscript and for helpful suggestions. ...
doi:10.1002/prot.10491
pmid:12945056
fatcat:tikiebccerhr3n2wqhqczrclu4
Distribution and Evolution of Circular Miniproteins in Flowering Plants
2008
The Plant Cell
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Cyclotides are disulfide-rich miniproteins with the unique structural features of a circular backbone and knotted arrangement of three conserved disulfide bonds. ...
This is strongly supported by recent findings on the in planta biosynthesis of cyclotides, which involves the serendipitous recruitment of ubiquitous proteolytic enzymes for cyclization. ...
Likewise, another common protein, protein disulfide isomerase, assists in folding of cyclotides (Gruber et al., 2007b) , and so it appears that no special coevolution of a folding and cyclization machinery ...
doi:10.1105/tpc.108.062331
pmid:18827180
pmcid:PMC2570719
fatcat:2q7amdc665difcdyltuolz54wa
PINIR: a comprehensive information resource for Pin-II type protease inhibitors
2021
BMC Plant Biology
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For each PI, the number and position for signature sequences are specified: 695 domains, 75 linkers, 63 reactive center loops, and 10 disulfide bond patterns are identified and mapped. ...
These features of Pin-II type PIs make them potential molecules for protein engineering and designing inhibitors for agricultural and therapeutic applications. ...
Sheon Mary, University of Glasgow, UK for suggestions to revise the English language of the manuscript. 1 ...
doi:10.1186/s12870-021-03027-0
pmid:34107869
fatcat:gwtql3gjdbdollbvrfv2fl7dwy
Evolution of Escherichia coli Expression System in Producing Antibody Recombinant Fragments
2020
International Journal of Molecular Sciences
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Antibodies and antibody-derived molecules are continuously developed as both therapeutic agents and key reagents for advanced diagnostic investigations. ...
Their application in these fields has indeed greatly expanded the demand of these molecules and the need for their production in high yield and purity. ...
Periplasmic proteins may encounter two types of protein folding catalysts: protein disulfide isomerases (Dsb proteins), which catalyze the formation of disulfide bonds, and peptidyl-prolyl isomerases ( ...
doi:10.3390/ijms21176324
pmid:32878291
pmcid:PMC7504322
fatcat:4z33ancld5alddn4riau67d4va
Peroxiredoxins wear many hats: Factors that fashion their peroxide sensing personalities
2021
Redox Biology
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In this review, we give a tabulated overview on what is known about human and bacterial peroxiredoxins with a focus on structure, PTMs, and protein-protein interactions. ...
Peroxiredoxins (Prdxs) sense and assess peroxide levels, and signal through protein interactions. ...
It is similar for Prdxs in determining their functional identity. ...
doi:10.1016/j.redox.2021.101959
pmid:33895094
fatcat:gqkgysr3hffevknpwpsge6dnwa
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