Molecular dynamics simulation of a psychrophilic adenylate kinase

다국어 초록 (Multilingual Abstract)

Proteins from psychrophilic organisms can function at low temperatures and have shown potential for industrial applications. In the present study, thermal denaturation of a psychrophilic adenylate kinase (AKpsychro) from Bacillus globisporus was measured using circular dichroism spectroscopy and its molecular dynamics (MD) simulations were performed. The results fromthe unfolding experiment andMD simulations of AKpsychro were compared with those of its mesophilic and thermophilic homologues to study the relationship between dynamic motion and the cold adaptation of proteins.

참고문헌 (Reference)

1 John DM, "van’t Hoff enthalpies without baselines" 9 : 1416-1419, 2000

2 Glaser P, "Zinc, a novel structural element found in the family of bacterial adenylate kinases" 31 : 3038-3043, 1992

3 Somero GN, "Temperature adaptation of enzymes: biological optimization through structure-function compromises" 9 : 1-29, 1978

4 Bae E, "Structures and analysis of highly homologous psychrophilic, mesophilic, and thermophilic adenylate kinases" 279 : 28202-28208, 2004

5 Bae E, "Roles of static and dynamic domains in stability and catalysis of adenylate kinase" 103 : 2132-2137, 2006

6 Feller G, "Psychrophilic enzymes: hot topics in cold adaptation" 1 : 200-208, 2003

7 Feller G, "Psychrophilic enzymes: from folding to function and biotechnology" 512840-, 2013

8 Feller G, "Protein stability and enzyme activity at extreme biological temperatures" 22 : 323101-, 2010

9 Papaleo E, "Protein flexibility in psychrophilic and mesophilic trypsins. Evidence of evolutionary conservation of protein dynamics in trypsin-like serine-proteases" 582 : 1008-1018, 2008

10 Wintrode PL, "Protein dynamics in a family of laboratory evolved thermophilic enzymes" 327 : 745-757, 2003

11 Reed CJ, "Protein adaptations in archaeal extremophiles" 2013 : 373275-, 2013

12 Kale´ L, "NAMD2: greater scalability for parallel molecular dynamics" 151 : 283-312, 1999

13 Grottesi A, "Molecular dynamics study of a hyperthermophilic and a mesophilic rubredoxin" 46 : 287-294, 2002

14 Feller G, "Life at low temperatures: is disorder the driving force?" 11 : 211-216, 2007

15 Bae E, "Identifying and engineering ion pairs in adenylate kinases. Insights from molecular dynamics simulations of thermophilic and mesophilic homologues" 280 : 30943-30948, 2005

16 MacKerell AD, "Empirical potential for molecular modeling and dynamics studies of proteins" 102 : 3586-3616, 1998

17 Margesin R, "Diversity and ecology of psychrophilic microorganisms" 162 : 346-361, 2011

18 Berry MB, "Crystal structures of Bacillus stearothermophilus adenylate kinase with bound Ap5A, Mg2? Ap5A, and Mn2? Ap5A reveal an intermediate lid position and six coordinate octahedral geometry for bound Mg2? and Mn2?" 32 : 275-288, 1998

19 Kundu S, "Comparative structural studies of psychrophilic and mesophilic protein homologues by molecular dynamics simulation" 27 : 871-880, 2009

20 Haney PJ, "Analysis of thermal stabilizing interactions in mesophilic and thermophilic adenylate kinases from the genus Methanococcus" 274 : 28453-28458, 1999

21 Moon S, "An integrated approach for thermal stabilization of a mesophilic adenylate kinase" 82 : 1947-1959, 2014

22 D’Amico S, "Activity-stability relationships in extremophilic enzymes" 278 : 7891-7896, 2003