Literature DB >> 16866533

Convergent dynamics in the protease enzymatic superfamily.

Vincenzo Carnevale1, Simone Raugei, Cristian Micheletti, Paolo Carloni.   

Abstract

Proteases regulate various aspects of the life cycle in all organisms by cleaving specific peptide bonds. Their action is so central for biochemical processes that at least 2% of any known genome encodes for proteolytic enzymes. Here we show that selected proteases pairs, despite differences in oligomeric state, catalytic residues, and fold, share a common structural organization of functionally relevant regions which are further shown to undergo similar concerted movements. The structural and dynamical similarities found pervasively across evolutionarily distant clans point to common mechanisms for peptide hydrolysis.

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Year:  2006        PMID: 16866533     DOI: 10.1021/ja060896t

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN: 0002-7863            Impact factor:   15.419


  21 in total

Review 1.  The interface of protein structure, protein biophysics, and molecular evolution.

Authors:  David A Liberles; Sarah A Teichmann; Ivet Bahar; Ugo Bastolla; Jesse Bloom; Erich Bornberg-Bauer; Lucy J Colwell; A P Jason de Koning; Nikolay V Dokholyan; Julian Echave; Arne Elofsson; Dietlind L Gerloff; Richard A Goldstein; Johan A Grahnen; Mark T Holder; Clemens Lakner; Nicholas Lartillot; Simon C Lovell; Gavin Naylor; Tina Perica; David D Pollock; Tal Pupko; Lynne Regan; Andrew Roger; Nimrod Rubinstein; Eugene Shakhnovich; Kimmen Sjölander; Shamil Sunyaev; Ashley I Teufel; Jeffrey L Thorne; Joseph W Thornton; Daniel M Weinreich; Simon Whelan
Journal:  Protein Sci       Date:  2012-04-23       Impact factor: 6.725

2.  Microseconds dynamics simulations of the outer-membrane protease T.

Authors:  Marilisa Neri; Marc Baaden; Vincenzo Carnevale; Claudio Anselmi; Amos Maritan; Paolo Carloni
Journal:  Biophys J       Date:  2007-09-07       Impact factor: 4.033

3.  Small- and large-scale conformational changes of adenylate kinase: a molecular dynamics study of the subdomain motion and mechanics.

Authors:  Francesco Pontiggia; Andrea Zen; Cristian Micheletti
Journal:  Biophys J       Date:  2008-10-17       Impact factor: 4.033

4.  Biocatalyst activity in nonaqueous environments correlates with centisecond-range protein motions.

Authors:  Ross K Eppler; Elton P Hudson; Shannon D Chase; Jonathan S Dordick; Jeffrey A Reimer; Douglas S Clark
Journal:  Proc Natl Acad Sci U S A       Date:  2008-10-07       Impact factor: 11.205

5.  Coarse-grained description of protein internal dynamics: an optimal strategy for decomposing proteins in rigid subunits.

Authors:  R Potestio; F Pontiggia; C Micheletti
Journal:  Biophys J       Date:  2009-06-17       Impact factor: 4.033

6.  Correspondences between low-energy modes in enzymes: dynamics-based alignment of enzymatic functional families.

Authors:  Andrea Zen; Vincenzo Carnevale; Arthur M Lesk; Cristian Micheletti
Journal:  Protein Sci       Date:  2008-03-27       Impact factor: 6.725

7.  Systematic study of anharmonic features in a principal component analysis of gramicidin A.

Authors:  Martin Kurylowicz; Ching-Hsing Yu; Régis Pomès
Journal:  Biophys J       Date:  2010-02-03       Impact factor: 4.033

8.  Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity.

Authors:  Márton Münz; Rune Lyngsø; Jotun Hein; Philip C Biggin
Journal:  BMC Bioinformatics       Date:  2010-04-14       Impact factor: 3.169

9.  ALADYN: a web server for aligning proteins by matching their large-scale motion.

Authors:  R Potestio; T Aleksiev; F Pontiggia; S Cozzini; C Micheletti
Journal:  Nucleic Acids Res       Date:  2010-05-05       Impact factor: 16.971

10.  Comparing interfacial dynamics in protein-protein complexes: an elastic network approach.

Authors:  Andrea Zen; Cristian Micheletti; Ozlem Keskin; Ruth Nussinov
Journal:  BMC Struct Biol       Date:  2010-08-08
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