title: Engineering Proteins for Thermostability with iRDP Web Server.
abstract: Engineering protein molecules with desired structure and biological functions has been an elusive goal. Development of industrially viable proteins with improved properties such as stability, catalytic activity and altered specificity by modifying the structure of an existing protein has widely been targeted through rational protein engineering. Although a range of factors contributing to thermal stability have been identified and widely researched, the in silico implementation of these as strategies directed towards enhancement of protein stability has not yet been explored extensively. A wide range of structural analysis tools is currently available for in silico protein engineering. However these tools concentrate on only a limited number of factors or individual protein structures, resulting in cumbersome and time-consuming analysis. The iRDP web server presented here provides a unified platform comprising of iCAPS, iStability and iMutants modules. Each module addresses different facets of effective rational engineering of proteins aiming towards enhanced stability. While iCAPS aids in selection of target protein based on factors contributing to structural stability, iStability uniquely offers in silico implementation of known thermostabilization strategies in proteins for identification and stability prediction of potential stabilizing mutation sites. iMutants aims to assess mutants based on changes in local interaction network and degree of residue conservation at the mutation sites. Each module was validated using an extensively diverse dataset. The server is freely accessible at http://irdp.ncl.res.in and has no login requirements.
authors.affiliation: Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, Maharashtra, 411008, India.
authors.forename: Priyabrata
authors.initials: P
authors.lastname: Panigrahi
authors.affiliation: Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, Maharashtra, 411008, India.
authors.forename: Manas
authors.initials: M
authors.lastname: Sule
authors.affiliation: Division of Chemical Engineering and Process Development, CSIR-National Chemical Laboratory, Pune, Maharashtra, 411008, India.
authors.forename: Avinash
authors.initials: A
authors.lastname: Ghanate
authors.affiliation: Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, Maharashtra, 411008, India.
authors.forename: Sureshkumar
authors.initials: S
authors.lastname: Ramasamy
authors.affiliation: Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, Maharashtra, 411008, India.
authors.forename: C G
authors.initials: CG
authors.lastname: Suresh
mesh_terms: D000596:Amino Acids / Q000737:chemistry; D003198:Computer Simulation; D030562:Databases, Protein; D015195:Drug Design; D006358:Hot Temperature; D057927:Hydrophobic and Hydrophilic Interactions; D020407:Internet; D008958:Models, Molecular; D011487:Protein Conformation; D011489:Protein Denaturation; D015202:Protein Engineering / Q000379:methods*; D055550:Protein Stability; D012984:Software; D013329:Structure-Activity Relationship; D013816:Thermodynamics; D014584:User-Computer Interface; D057188:Workflow
chemical_list: D000596:Amino Acids