Identification of protein stability patches that pinpoint key structural or functional sites
Pages 521 - 523
Abstract
The ability to locate in silico, in a protein structure, the active site, the binding site or the initiation site of conformational changes is important for understanding the functional mechanisms and is a prerequisite for the rational prediction of targeted mutations or for protein design. The amino acids in these sites have been optimized during evolution to fulfill a specific function, but not necessarily to improve stability. We present a program able to detect residues that are optimal or non-optimal against thermodynamic stability and to group them into patches. We apply this program to bovine seminal ribonuclease, a member of a well-studied enzyme family that binds RNA and undergoes 3D domain swapping under certain conditions.
References
[1]
Polacco BJ and Babbitt PC. 2006. Automated discovery of 3D motifs for protein function annotation. Bioinformatics 22 (2006), 723--730.
[2]
Zhang C. and Kim S. 2003. Overview of structural genomics: from structure to function. Curr Opin Chem Biol 7 (2003) 28--32.
[3]
Laskowski R A, Watson J D, Thornton J M (2005). ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res. 33 (2005) W89--W93.
[4]
Innis, CA. and Sowdhamini, AP. 2004. Prediction of functional sites in proteins using conserved functional group analysis. J Mol Biol 337, 4 (Apr. 2004), 1053--1068.
[5]
Gerlt JA.and Babbitt PC. 2000. Can sequence determine function? Genome Biol. 1, 5 (Nov. 2000), Reviews0005.
[6]
Dehouck Y., Gilis D., Rooman M. 2006. A New Generation of Statistical Potentials for Proteins. Biophysical J. 90 (June 2006) 4010--4017.
[7]
Libonati M. and Floridi A. 1969. Breakdown of double-stranded RNA by bull semen ribonuclease. Eur J Biochem. 8,1 (mar 1969) 81--87.
[8]
Mazzarella L., Capasso S., Demasi D., Di Lorenzo G., Mattia CA, Zagari A. Bovine seminal ribonuclease: structure at 1.9 A resolution. Acta Crystallogr D Biol Crystallogr. 1, 49(Jul 1993) 389--402.
[9]
Berisio R., Sica F., De Lorenzo C., Di Fiore A., Piccoli R., Zagari A., Mazzarella L., 2003. Crystal structure of the dimeric unswapped form of bovine seminal ribonuclease. FEBS Lett. 6, 554 (Nov 2003)105--110.
[10]
Di Donato A., Ciardiello MA., de Nigris M., Piccoli R., Mazzarella L., D'Alessio G. 1993. Selective deamination of ribonuclease A. Isolation and characterization of the resulting isoaspartyl and aspartyl derivatives. J Biol Chem. 5, 268 (Mar 1993) 4745--4751
[11]
Dehouck Y., Biot C., Gilis D., Kwasigroch J. M., Rooman M. 2003. Sequence-structure signals of 3D domain swapping. J. Mol. Biol. 330 (2003) 1215--1225.
Index Terms
- Identification of protein stability patches that pinpoint key structural or functional sites
Recommendations
Identification and Analysis of Key Residues in Protein–RNA Complexes
Protein–RNA complexes play important roles in various biological processes. The functions of protein–RNA complexes are dictated by their interactions, binding, stability, and affinity. In this work, we have identified the key residues KRs, which are ...
Predicting protein interaction sites: binding hot-spots in protein--protein and protein--ligand interfaces
Motivation: Protein assemblies are currently poorly represented in structural databases and their structural elucidation is a key goal in biology. Here we analyse clefts in protein surfaces, likely to correspond to binding 'hot-spots', and rank them ...
Comments
Please enable JavaScript to view thecomments powered by Disqus.Information & Contributors
Information
Published In
October 2012
725 pages
ISBN:9781450316705
DOI:10.1145/2382936
- General Chair:
- Sanjay Ranka,
- Program Chairs:
- Tamer Kahveci,
- Mona Singh
Copyright © 2012 Authors.
Sponsors
Publisher
Association for Computing Machinery
New York, NY, United States
Publication History
Published: 07 October 2012
Check for updates
Author Tags
Qualifiers
- Poster
Conference
BCB' 12
Sponsor:
BCB' 12: ACM International Conference on Bioinformatics, Computational Biology and Biomedicine
October 7 - 10, 2012
Florida, Orlando
Acceptance Rates
BCB '12 Paper Acceptance Rate 33 of 159 submissions, 21%;
Overall Acceptance Rate 254 of 885 submissions, 29%
Upcoming Conference
Contributors
Other Metrics
Bibliometrics & Citations
Bibliometrics
Article Metrics
- 0Total Citations
- 50Total Downloads
- Downloads (Last 12 months)0
- Downloads (Last 6 weeks)0
Reflects downloads up to 29 Sep 2024
Other Metrics
Citations
View Options
Get Access
Login options
Check if you have access through your login credentials or your institution to get full access on this article.
Sign in