SPROUTS: a database for the evaluation of protein stability upon point mutation

SPROUTS (Structural Prediction for pRotein fOlding UTility System) is a new database that provides access to various structural data sets and integrated functionalities not yet available to the community. The originality of the SPROUTS database is the ability to gain access to a variety of structural analyses at one place and with a strong interaction between them. SPROUTS currently combines data pertaining to 429 structures that capture representative folds and results related to the prediction of critical residues expected to belong to the folding nucleus: the MIR (Most Interacting Residues), the description of the structures in terms of modular fragments: the TEF (Tightened End Fragments), and the calculation at each position of the free energy change gradient upon mutation by one of the 19 amino acids. All database results can be displayed and downloaded in textual files and Excel spreadsheets and visualized on the protein structure. SPROUTS is a unique resource to access as well as visualize state-of-the-art characteristics of protein folding and analyse the effect of point mutations on protein structure. It is available at http://bioinformatics.eas.asu.edu/sprouts.html.

[1]  S. Marqusee,et al.  A rapid test for identification of autonomous folding units in proteins. , 2000, Journal of molecular biology.

[2]  E. Haas,et al.  Nonlocal interactions stabilize long range loops in the initial folding intermediates of reduced bovine pancreatic trypsin inhibitor. , 1995, Biochemistry.

[3]  Shuangye Yin,et al.  Eris: an automated estimator of protein stability , 2007, Nature Methods.

[4]  Anne Poupon,et al.  Predicting the protein folding nucleus from a sequence , 1999, FEBS letters.

[5]  A. Fersht,et al.  Phi-value analysis and the nature of protein-folding transition states. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[6]  Iosif I. Vaisman,et al.  Accurate prediction of stability changes in protein mutants by combining machine learning with structure based computational mutagenesis , 2008, Bioinform..

[7]  Hongyi Zhou,et al.  Distance‐scaled, finite ideal‐gas reference state improves structure‐derived potentials of mean force for structure selection and stability prediction , 2002, Protein science : a publication of the Protein Society.

[8]  A. Fersht.  Nucleation mechanisms in protein folding. , 1997, Current opinion in structural biology.

[9]  Jacques Chomilier,et al.  RPBS: a web resource for structural bioinformatics , 2005, Nucleic Acids Res..

[10]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[11]  D Gilis,et al.  PoPMuSiC, an algorithm for predicting protein mutant stability changes: application to prion proteins. , 2000, Protein engineering.

[12]  Motonori Ota,et al.  The Protein Mutant Database , 1999, Nucleic Acids Res..

[13]  Ashley M. Buckle,et al.  Protein Folding Database (PFD 2.0): an online environment for the International Foldeomics Consortium , 2006, Nucleic Acids Res..

[14]  Arlo Z. Randall,et al.  Prediction of protein stability changes for single‐site mutations using support vector machines , 2005, Proteins.

[15]  Jacques Chomilier,et al.  Universal positions in globular proteins. , 2004, European journal of biochemistry.

[16]  Akinori Sarai,et al.  ProTherm and ProNIT: thermodynamic databases for proteins and protein–nucleic acid interactions , 2005, Nucleic Acids Res..

[17]  R. Jernigan,et al.  Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. , 1996, Journal of molecular biology.

[18]  E. Trifonov,et al.  Closed loops of nearly standard size: common basic element of protein structure , 2000, FEBS letters.

[19]  A. Poupon,et al.  Populations of hydrophobic amino acids within protein globular domains: Identification of conserved “topohydrophobic” positions , 1998, Proteins.

[20]  François Stricher,et al.  The FoldX web server: an online force field , 2005, Nucleic Acids Res..

[21]  M. Michael Gromiha,et al.  CUPSAT: prediction of protein stability upon point mutations , 2006, Nucleic Acids Res..

[22]  I. Berezovsky,et al.  Distribution of tightened end fragments of globular proteins statistically matches that of topohydrophobic positions: towards an efficient punctuation of protein folding? , 2001, Cellular and Molecular Life Sciences CMLS.

[23]  Piero Fariselli,et al.  I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure , 2005, Nucleic Acids Res..