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Finding of residues crucial for supersecondary structure formation

Alexander E. Kister, Israel Gelfand
2009 Proceedings of the National Academy of Sciences of the United States of America  
Structure-based alignment revealed that 30 -35% of the positions in the sequences in each group of proteins are "conserved positions" occupied either by hydrophobic-only or hydrophilic-only residues.  ...  The algorithm is based on the alignment of residues that form hydrogen bonds between corresponding strands.  ...  Step 1: Selection of Representative Proteins and Their Sequence Alignment. The selection of representatives is based on SCOP structural classification.  ... 
doi:10.1073/pnas.0909714106 pmid:19855006 pmcid:PMC2776455 fatcat:6amjg4mnunalblzku4vqqdeubq

Chemical composition is maintained in poorly conserved intrinsically disordered regions and suggests a means for their classification

Harry Amri Moesa, Shunichi Wakabayashi, Kenta Nakai, Ashwini Patil
2012 Molecular Biosystems  
Clustering disordered regions based on their chemical composition resulted in functionally distinct groups.  ...  However, given their lack of structure and sequence conservation, the means through which they stay functional is not clear.  ...  The current domain classification techniques are based either on structure 18 or on sequence conservation. 17 Due to their lack of structure and sequence conservation, a large number of IDRs are not  ... 
doi:10.1039/c2mb25202c pmid:23076520 fatcat:25sur7zpyrcftgfsqktgvjxu4u

Classification of the human THAP protein family identifies an evolutionarily conserved coiled coil region

Hiral M. Sanghavi, Sairam S. Mallajosyala, Sharmistha Majumdar
2019 BMC Structural Biology  
However, the carboxy terminus of most THAP proteins is yet to be structurally characterized. A coiled coil region is known to help in protein oligomerization in THAP1 and THAP11.  ...  It is not known if other human THAP proteins oligomerize. We have used bioinformatic tools to explore the possibility of dimerization of THAP proteins via a coiled coil region.  ...  whereas Pfam [39] is a database based on amino acid sequence based classification.  ... 
doi:10.1186/s12900-019-0102-2 pmid:30836974 pmcid:PMC6402169 fatcat:ioqkbefrkreo3iyxfxkh63mgmu


2006 Journal of Bioinformatics and Computational Biology  
Hydrophobic clusters on some protein-DNA and protein-protein interfaces were also analyzed.  ...  The conserved hydrophobic core is an important feature of a family of protein domains. We suggest a procedure for finding and the analysis of conserved hydrophobic cores.  ...  In the present work we propose a method, based on the usage of CluD program, for the detection of conserved hydrophobic clusters both in protein structures (the "conserved hydrophobic core" of a domain  ... 
doi:10.1142/s0219720006001837 pmid:16819788 fatcat:kxfvvbnie5fqbm4olnikoq4eoe

Structural bioinformatics analysis of free cysteines in protein environments

Sheau Ling Ho, Andrew H.-J. Wang
2009 Journal of the Taiwan Institute of Chemical Engineers / Elsevier  
This study is focused on the discrimination between structural versus active free cysteines based on a local environment analysis which does not appear to have been attempted previously.  ...  contacts to hydrophobic residues and lower amount of contacts to polar or charged residues.  ...  Conserved residues mapping on certain characteristics may likewise identify a key site or perhaps a sensible function. Accordingly, the approaches we have presented were based on the structures.  ... 
doi:10.1016/j.jtice.2008.07.015 pmid:32288881 pmcid:PMC7102755 fatcat:mjztsl2yxnd23motirdfkbbkca

The immunoglobulin fold family: sequence analysis and 3D structure comparisons

D.M. Halaby, A. Poupon, J.-P. Mornon
1999 Protein Engineering Design & Selection  
Based upon sequence and structure analysis, we propose the introduction of two new subtypes (C3 and C4) to the previous classifications, in addition to a new global structural classification.  ...  Finally, this review suggest that hydrophobic residues constituting the common hydrophobic cores are important clues to explain how highly divergent sequences can adopt a similar fold.  ...  Burial of conserved hydrophobic residues Based on the structural alignment a typical hydrophobic core of the Ig fold can be described.  ... 
doi:10.1093/protein/12.7.563 pmid:10436082 fatcat:bkwt4gckj5fyfkt33xqrcuj6ni

Amino acid residue: is it structural or functional?

Alexander P. Golovanov, Roman G. Efremov, Victor A. Jaravine, Gérard Vergoten, Alexander S. Arseniev
1995 FEBS Letters  
A new approach is suggested for delineating the structural and functional amino acid residues in proteins with known three-dimensional structure, basing on the involvement of residues in intramolecular  ...  hydrophobic and hydrophilic interactions and additional information about the conservativity of the residues.  ...  The method is based on the analysis of the hydrophobic and hydrophilic contacts between amino acid residues in protein molecules with the help of molecular hydrophobicity potential (MHP).  ... 
doi:10.1016/0014-5793(95)01212-w pmid:7498470 fatcat:yz7qxndjafb6pp3oldd4zfbrgu

Armadillo Motifs Involved in Vesicular Transport

Harald Striegl, Miguel A. Andrade-Navarro, Udo Heinemann, Andreas Hofmann
2010 PLoS ONE  
Here we describe the p115 ARM-motifs for reasons of clarity and nomenclature and show that both sequence and structure are highly conserved among ARM-repeat proteins.  ...  They contain an imperfect repeating sequence motif that forms a conserved three-dimensional structure.  ...  Figure production: All pictures of protein structures were prepared using PyMOL [31] . The structure based sequence alignment was prepared using the DaliLite program [32] . Author Contributions  ... 
doi:10.1371/journal.pone.0008991 pmid:20126549 pmcid:PMC2813876 fatcat:vcui5wp2pjgqva6u27qo67ckqy

Construction and analysis of a plant non-specific lipid transfer protein database (nsLTPDB)

Nai-Jyuan Wang, Chi-Ching Lee, Chao-Sheng Cheng, Wei-Cheng Lo, Ya-Fen Yang, Ming-Nan Chen, Ping-Chiang Lyu
2012 BMC Genomics  
Results: Meanwhile, bioinformatics and statistics methods were implemented to develop a classification method for nsLTPs based on the patterns of the eight highly-conserved cysteine residues, and to suggest  ...  Plant non-specific lipid transfer proteins (nsLTPs) are small and basic proteins.  ...  Based on the number of residues that intervene the eight conserved cysteine residues, the 595 nsLTPs were clustered into 5 different groups.  ... 
doi:10.1186/1471-2164-13-s1-s9 pmid:22369214 pmcid:PMC3303721 fatcat:znishtjw2bhq3jvqnj5h2jbe3q

A simple approach for protein structure discrimination based on the network pattern of conserved hydrophobic residues

Usha K. Muppirala, Zhijun Li
2006 Protein Engineering Design & Selection  
Evolutionarily conserved hydrophobic residues at the core of protein structures are generally assumed to play a structural role in protein folding and stability.  ...  In this work, we explored the possibility of employing this feature of native structures for discriminating non-native structures from native ones.  ...  Lybrand at Vanderbilt University for comments on the manuscript. This work was supported by the starting fund from University of the Sciences in Philadelphia.  ... 
doi:10.1093/protein/gzl009 pmid:16565147 fatcat:5eqpsal5qrb53p22qhjof3d45u

Common fold in helix-hairpin-helix proteins

X. Shao
2000 Nucleic Acids Research  
(HhH) 2 domains show clear structural integrity and a conserved hydrophobic core composed of seven residues, one residue from each α-helix and each hairpin, and deserves recognition as a distinct protein  ...  Statistically significant sequence similarity of HhH motifs and pronounced structural conservation argue for homology between (HhH) 2 domains in different protein families.  ...  Additional conserved hydrophobic residues are shown in bold. Figure 3 . 3 Conserved hydrophobic core residues in the (HhH) 2 proteins and DNA binding by HhH proteins.  ... 
doi:10.1093/nar/28.14.2643 pmid:10908318 pmcid:PMC102670 fatcat:27pebojdq5blhkb45dpihmpt54

Progress and challenges in predicting protein-protein interaction sites

I. Ezkurdia, L. Bartoli, P. Fariselli, R. Casadio, A. Valencia, M. L. Tress
2008 Briefings in Bioinformatics  
Proteins in complexes are still under-represented in the structural databases and in particular many proteins involved in transient complexes are still to be crystallized.  ...  In recent years a significant number of methods have been developed to predict these interface residues and here we review the current status of the field.  ...  [35] and confirm that predictors can make fairly reliable predictions for protein-protein-binding residues based on a limited set of structure-based features.  ... 
doi:10.1093/bib/bbp021 pmid:19346321 fatcat:35bckwqpejad5dt2bn3owas4v4

Profile combinatorics for fragment selection in comparative protein structure modeling

D.J. Sweeney, G.M. Alter, M.L. Raymer, T.E. Doom
2001 Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001)  
Contemporary protein structure prediction algorithms represent the sequence of every protein of known structure with a profile to which the profile of a protein sequence of unknown structure is compared  ...  Equivalent substructures can then be swapped on the common regions to generate an array of profiles which represent hypothetical structures to supplement profiles of known structures.  ...  Hydrophobic residues 'hide' from water with other hydrophobic residues, and they tend to be conserved in positions where this molecular 'glue' increases the stability of the protein.  ... 
doi:10.1109/bibe.2001.974439 dblp:conf/bibe/SweeneyARD01 fatcat:atg6qnvdonco3m5b5yux4z4qiu

A survey of available tools and web servers for analysis of protein-protein interactions and interfaces

N. Tuncbag, G. Kar, O. Keskin, A. Gursoy, R. Nussinov
2008 Briefings in Bioinformatics  
His research focuses on the computational studies of protein interactions and parallel computing.  ...  Her research focuses on the computational studies of protein interactions and dynamics. Attila Gursoy is an associate professor at .  ...  ConSurf [65, 66] is a web server, which incorporates several phylogenetic-based algorithms [67] to predict conservation scores of residues for a given protein structure.  ... 
doi:10.1093/bib/bbp001 pmid:19240123 pmcid:PMC2671387 fatcat:e2q7s5y7zrfmnnkp4l6yjkr32u

Cysteine Function Governs Its Conservation and Degeneration and Restricts Its Utilization on Protein Surfaces

Stefano M. Marino, Vadim N. Gladyshev
2010 Journal of Molecular Biology  
Whereas free Cys is a polar amino acid, Cys in proteins is often buried and its classification on the hydrophobicity scale is ambiguous.  ...  In addition, clustering of Cys with another Cys residue was associated with high conservation, whereas exposure of Cys on protein surface with low conservation.  ...  These classifications are based on, even if not always strictly limited to [8] , the analysis of 3D structures of proteins and define the hydrophobic character as the tendency for a residue to be found  ... 
doi:10.1016/j.jmb.2010.09.027 pmid:20950627 pmcid:PMC3061813 fatcat:gsegr7q6szbxpiv6cjuk2i3p6m
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