Environment specific substitution tables for thermophilic proteins
نویسندگان
چکیده
منابع مشابه
Environment specific substitution tables improve membrane protein alignment
MOTIVATION Membrane proteins are both abundant and important in cells, but the small number of solved structures restricts our understanding of them. Here we consider whether membrane proteins undergo different substitutions from their soluble counterparts and whether these can be used to improve membrane protein alignments, and therefore improve prediction of their structure. RESULTS We cons...
متن کاملUlla: a program for calculating environment-specific amino acid substitution tables
SUMMARY Amino acid residues are under various kinds of local environmental restraints, which influence substitution patterns. Ulla,(1) a program for calculating environment-specific substitution tables, reads protein sequence alignments and local environment annotations. The program produces a substitution table for every possible combination of environment features. Sparse data is handled usin...
متن کاملIdentification of specificity determining residues in enzymes using environment specific substitution tables
Environment speci c substitution tables have been used e ectively for distinguishing structural and functional constraints on proteins and thereby identify their active sites (Chelliah et al. (2004)). This work explores whether a similar approach can be used to identify speci city determining residues (SDRs) responsible for cofactor dependence, substrate speci city or subtle catalytic variation...
متن کاملProteins from thermophilic microorganisms.
INTRODUCTION .......... ....................................... 320 THE THERMOPHILIC MICROORGANISMS .......... ......................... 321 POSSIBLE MECHANISMS OF SURVIVAL .......... .......................... 322 Lipids ................................................. 322 Rapid Resynthesis ............ ..................................... 322 Thermally Stable Macromolecules ...................
متن کاملHydrophobic environment is a key factor for the stability of thermophilic proteins.
The stability of thermophilic proteins has been viewed from different perspectives and there is yet no unified principle to understand this stability. It would be valuable to reveal the most important interactions for designing thermostable proteins for such applications as industrial protein engineering. In this work, we have systematically analyzed the importance of various interactions by co...
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ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2007
ISSN: 1471-2105
DOI: 10.1186/1471-2105-8-s1-s15