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Planning combinatorial disulfide cross-links for protein fold determination

Fei Xiong, Alan M Friedman, Chris Bailey-Kellogg
2011 BMC Bioinformatics  
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

Xiaoduan Ye, Patrick K. O'Neil, Adrienne N. Foster, Michal J. Gajda, Jan Kosinski, Michal A. Kurowski, Janusz M. Bujnicki, Alan M. Friedman, Chris Bailey-Kellogg
2009 Protein Science  
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

Andre L. Samson, Anja S. Knaupp, Itamar Kass, Oded Kleifeld, Emilia M. Marijanovic, Victoria A. Hughes, Chris J. Lupton, Ashley M. Buckle, Stephen P. Bottomley, Robert L. Medcalf
2014 Journal of Biological Chemistry  
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

Valerie N. Olmo, Eric Grote
2009 Journal of Biological Chemistry  
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

Mahta Nili, Aditi Mukherjee, Ujwal Shinde, Larry David, Peter Rotwein
2011 Journal of Biological Chemistry  
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]

Ron Piran, Ehud Keinan
2005 Catalytic Antibodies  
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

Mirfath Sultana Mesbahuddin, Aravindhan Ganesan, Subha Kalyaanamoorthy, Roberto Chica
2021 Protein Engineering Design & Selection  
Targeted inhibition of misregulated proteinprotein 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 proteinprotein 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

D MASTELLOS
2004 Molecular Immunology  
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

D MASTELLOS
2004 Molecular Immunology  
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

Subhashini Srinivasan, Carl J. March, Sucha Sudarsanam
2008 Protein Science  
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

Buddhadeb Mallik, John D. Lambris, Dimitrios Morikis
2003 Proteins: Structure, Function, and Bioinformatics  
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

C. W. Gruber, A. G. Elliott, D. C. Ireland, P. G. Delprete, S. Dessein, U. Goransson, M. Trabi, C. K. Wang, A. B. Kinghorn, E. Robbrecht, D. J. Craik
2008 The Plant Cell  
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

Nikhilesh K. Yadav, Nidhi S. Saikhedkar, Ashok P. Giri
2021 BMC Plant Biology  
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

Annamaria Sandomenico, Jwala P. Sivaccumar, Menotti Ruvo
2020 International Journal of Molecular Sciences  
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

Jesalyn Bolduc, Katarina Koruza, Ting Luo, Julia Malo Pueyo, Trung Nghia Vo, Daria Ezeriņa, Joris Messens
2021 Redox Biology  
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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