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Predictive and Experimental Approaches for Elucidating Protein–Protein Interactions and Quaternary Structures

John Nealon, Limcy Philomina, Liam McGuffin
2017 International Journal of Molecular Sciences  
Abstract: The elucidation of protein-protein interactions is vital for determining the function and action of quaternary protein structures.  ...  We suggest a fusion of experimental and predictive methods that make use of sparse experimental data to determine higher resolution predicted protein interactions as being necessary to drive forward development  ...  means that a reliable generic quaternary structure model quality assessment method has yet to be developed.  ... 
doi:10.3390/ijms18122623 pmid:29206185 pmcid:PMC5751226 fatcat:6ffy3cv2hzdvtf5kgvwitl3toy

Structural Bioinformatics of Proteins: Predicting the Tertiary and Quaternary Structure of Proteins from Sequence [chapter]

Baldo Oliva, Joan Planas-Iglesias, Jaume Bonet, Manuel A., Elisenda Feliu, Attila Gursoy
2012 Protein-Protein Interactions - Computational and Experimental Tools  
This scoring function, termed knowledge-based or statistical potential, works as a coarse-grained descriptor of the environment of the protein, and can be used to assess the quality of a protein 3D model  ...  Among these scoring functions, statistical potential is a term that refers to a knowledge-based scoring function that depends on specific properties of known protein-protein interactions stored in some  ... 
doi:10.5772/37856 fatcat:2yoie6jvavcdnedcytg4iyfnqi

Assessment of protein assembly prediction in CASP13

Dmytro Guzenko, Aleix Lafita, Bohdan Monastyrskyy, Andriy Kryshtafovych, Jose M. Duarte
2019 Proteins: Structure, Function, and Bioinformatics  
We present the assembly category assessment in the 13th edition of the CASP community-wide experiment. For the second time, protein assemblies constitute an independent assessment category.  ...  Compared to the last edition we see a clear uptake in participation, more oligomeric targets released, and consistent, albeit modest, improvement of the predictions quality.  ...  At the other extreme are transient protein-protein complexes where the association is opportunistic and promiscuous, representing the functions of the proteins involved [8] .  ... 
doi:10.1002/prot.25795 pmid:31374138 pmcid:PMC6851419 fatcat:63go5vdj6jawni2evisq26oexi

GalaxyGemini: a web server for protein homo-oligomer structure prediction based on similarity

Hasup Lee, Hahnbeom Park, Junsu Ko, Chaok Seok
2013 Computer applications in the biosciences : CABIOS  
A large number of proteins function as homooligomers; therefore, predicting homo-oligomeric structure of proteins is of primary importance for understanding protein function at the molecular level.  ...  The server takes a protein monomer structure as input and predicts its homooligomer structure from oligomer templates selected based on sequence and tertiary/quaternary structure similarity.  ...  Knowledge of the protein oligomeric state is therefore crucial for understanding protein function at the molecular level.  ... 
doi:10.1093/bioinformatics/btt079 pmid:23413437 fatcat:inbnsylzvjdbzah37p56n4yqb4

Predicted binding site information improves model ranking in protein docking using experimental and computer-generated target structures

Surabhi Maheshwari, Michal Brylinski
2015 BMC Structural Biology  
The scoring function implemented in eRank PPI employs multiple features including interface probability estimates calculated by eFindSite PPI and a novel contact-based symmetry score.  ...  Protein-protein interactions (PPIs) mediate the vast majority of biological processes, therefore, significant efforts have been directed to investigate PPIs to fully comprehend cellular functions.  ...  Consequently, the structural characterization of protein-protein complexes provides valuable insights into protein function and association mechanisms, immensely contributing to the understanding of cellular  ... 
doi:10.1186/s12900-015-0050-4 pmid:26597230 pmcid:PMC4657198 fatcat:lbvpqn4o4zhcxcm7niop7dhsca

Investigation of protein quaternary structure via stoichiometry and symmetry ınformation

Selcuk Korkmaz, Jose M. Duarte, Andreas Prlić, Dincer Goksuluk, Gokmen Zararsiz, Osman Saracbasi, Stephen K. Burley, Peter W. Rose, Yang Zhang
2018 PLoS ONE  
We have developed a freely-available web-based tool to make this approach accessible to researchers and PDB Biocurators (http://quatstruct.rcsb.org/).  ...  Further investigation is, therefore, needed to evaluate the correctness of quaternary structure annotations.  ...  We also thank Eugene Krissinel for explaining usage of the PISA software. Author Contributions  ... 
doi:10.1371/journal.pone.0197176 pmid:29864163 pmcid:PMC5986128 fatcat:jcxnup5fxjfslau3isu3s67jri

Protein Interaction Z Score Assessment (PIZSA): an empirical scoring scheme for evaluation of protein-protein interactions

2019 Nucleic Acids Research  
Our web server, PIZSA (http://cospi.iiserpune.ac.in/pizsa), assesses the likelihood of protein-protein interactions by assigning a Z Score computed from interface residue contacts.  ...  The PIZSA server is easy to use and could be used to score any input three-dimensional structure and provide a residue pair-wise break up of the results.  ...  ACKNOWLEDGEMENTS We would like to thank members of the COSPI lab at IISER Pune for valuable discussions and insights.  ... 
doi:10.1093/nar/gkz368 pmid:31114890 pmcid:PMC6602501 fatcat:24nfxwzosjbsrcysyxekx7ezam

Quaternary structure evaluation tool for protein assemblies [article]

Selcuk Korkmaz, Jose M Duarte, Andreas Prlic, Dincer Goksuluk, Gokmen Zararsiz, Osman Saracbasi, Stephen K Burley, Peter W Rose
2017 bioRxiv   pre-print
We have developed a freely-available web-based tool to make this approach accessible to researchers and PDB Biocurators (http://quatstruct.rcsb.org).  ...  Further investigation is, therefore, needed to evaluate the correctness of quaternary structure annotations.  ...  Symmetry is another important feature of protein tertiary and quaternary structure [12] and plays a key role in understanding protein evolution and structure/function relationships [3] , [12] , [13  ... 
doi:10.1101/224196 fatcat:5liut4cl5vbr3habhl63wgnaua

A knowledge-based scoring function to assess the stability of quaternary protein assemblies [article]

Abhilesh S Dhawanjewar, Ankit A Roy, Mallur S Madhusudhan
2019 bioRxiv   pre-print
Results: Our method, PIZSA (Protein Interaction Z Score Assessment) is a binary classification scheme for identification of stable protein quaternary assemblies (binders/non-binders) based on statistical  ...  In silico predictions of protein interactions entail sampling different conformations of the purported complex and then scoring these to assess for interaction viability.  ...  Acknowledgements We would like to thank members of the COSPI lab at IISER Pune for valuable discussions and insights.  ... 
doi:10.1101/562520 fatcat:udunch3gf5erze4c3qxxc7dnzu

Automated evaluation of quaternary structures from protein crystals [article]

Spencer Bliven, Aleix Lafita, Althea Parker, Guido Capitani, Jose M Duarte
2017 biorxiv/medrxiv   pre-print
A correct assessment of the quaternary structure of proteins is a fundamental prerequisite to understanding their function, physico-chemical properties and mode of interaction with other proteins.  ...  scoring.  ...  Acknowledgments G.C. initiated and led the research, contributing to the initial versions of the manuscript. Tragically he sickened and passed away on the 2nd of May 2017.  ... 
doi:10.1101/224717 fatcat:v4tnl2ovirdjxpjl4cl72pnpem

Automated evaluation of quaternary structures from protein crystals

Spencer Bliven, Aleix Lafita, Althea Parker, Guido Capitani, Jose M. Duarte, Roland L. Dunbrack
2018 PLoS Computational Biology  
A correct assessment of the quaternary structure of proteins is a fundamental prerequisite to understanding their function, physico-chemical properties and mode of interaction with other proteins.  ...  scoring.  ...  , contributing to the initial versions of the manuscript.  ... 
doi:10.1371/journal.pcbi.1006104 pmid:29708963 pmcid:PMC5945228 fatcat:ujak2j6c2vghji3jpnqmk3fbgy

Multimeric Threading-Based Prediction of Protein-Protein Interactions on a Genomic Scale: Application to the Saccharomyces cerevisiae Proteome

L. Lu
2003 Genome Research  
This article must therefore be hereby marked "advertisement" in accordance with 18 USC section 1734 solely to indicate this fact.  ...  We thank Peer Bork and Christian von Mering for generously providing us with some of the interaction data. The publication costs of this article were defrayed in part by payment of page charges.  ...  in the associated quaternary structure.  ... 
doi:10.1101/gr.1145203 pmid:12799350 pmcid:PMC403642 fatcat:j6jt6x5ssrbwzp3r4ckkmmncf4

CapsidMaps: Protein–protein interaction pattern discovery platform for the structural analysis of virus capsids using Google Maps

Mauricio Carrillo-Tripp, Daniel Jorge Montiel-García, Charles L. Brooks, Vijay S. Reddy
2015 Journal of Structural Biology  
CapsidMaps also facilitates the comparison of quaternary interactions between two spherical virus particles by computing a similarity (S)-score.  ...  Structural analysis and visualization of protein-protein interactions is a challenging task since it is difficult to appreciate easily the extent of all contacts made by the residues forming the interfaces  ...  In this way, the S-score is a valuable metric to quantitatively assess the similarity in quaternary interactions and subunit environments between two capsids.  ... 
doi:10.1016/j.jsb.2015.02.003 pmid:25697908 pmcid:PMC4750372 fatcat:b4cbx7ujhnhcxhegnrl6lfpidq

Interaction interfaces of protein domains are not topologically equivalent across families within superfamilies: Implications for metabolic and signaling pathways

N. Rekha, S.M. Machado, C. Narayanan, A. Krupa, N. Srinivasan
2004 Proteins: Structure, Function, and Bioinformatics  
Based on the analysis of multidomain proteins of known or unknown structure, we suggest that variation in protein-protein interactions in members within a superfamily could serve as diverging points in  ...  This variation in the location of interface happens in protein domains involved in a wide range of functions, such as enzymes, adapters, and domains that bind protein ligands, or cofactors.  ...  ACKNOWLEDGMENTS Our thanks to Anirban Bhaduri for kindly providing us with the superfamily alignments and superpositions in the PASS2 database, to Shashi Pandit for providing flat files of the SUPFAM database  ... 
doi:10.1002/prot.20319 pmid:15562516 fatcat:mjmrku4fubf4babdungf2cksdu

Machine Learning Methods for Protein Structure Prediction

Jianlin Cheng, A.N. Tegge, P. Baldi
2008 IEEE Reviews in Biomedical Engineering  
; 2-D prediction of spatial relationships between amino acids; 3-D prediction of the tertiary structure of a protein; and 4-D prediction of the quaternary structure of a multiprotein complex.  ...  A diverse set of both supervised and unsupervised machine learning methods has been applied over the years to tackle these problems and has significantly contributed to advancing the state-of-the-art of  ...  The assessment results are published in the supplemental issues of the journal Proteins. To date, the most successful structure prediction methods have been knowledge based.  ... 
doi:10.1109/rbme.2008.2008239 pmid:22274898 fatcat:4zx2zv2tojamtm6bruuuby2kbi
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