✦ LIBER ✦

Serine proteases: An ab initio molecular dynamics study

✍ Scribed by L. De Santis; P. Carloni

Publisher: John Wiley and Sons
Year: 1999
Tongue: English
Weight: 282 KB
Volume: 37
Category: Article
ISSN: 0887-3585
DOI: 10.1002/(sici)1097-0134(19991201)37:4<611::aid-prot11>3.0.co;2-7

No coin nor oath required. For personal study only.

✦ Synopsis

In serine proteases (SPs), the Hbond between His57 and Asp102 and that between Gly193 and the transition state intermediate play a crucial role in enzymatic function. To shed light on the nature of these interactions, we have carried out ab initio molecular dynamics simulations on complexes representing adducts between the reaction intermediate and elastase (one protein belonging to the SP family). Our calculations indicate the presence of a low-barrier H-bond between His57 and Asp102, in complete agreement with NMR experiments on enzyme-transition state analogue complexes. 1 Comparison with an ab initio molecular dynamics simulation on a model of the substrateenzyme adduct indicates that the Gly193-induced strong stabilization of the intermediate is accomplished by charge/dipole interactions and not by H-bonding as previously suggested. Inclusion of the protein electric field in the calculations does not affect significantly the charge distribution.

📜 SIMILAR VOLUMES

Ab initio molecular dynamics calculation

Ab initio molecular dynamics calculations to study catalysis

✍ K. Schwarz; E. Nusterer; P. Margl; P. E. Blöchl 📂 Article 📅 1997 🏛 John Wiley and Sons 🌐 English ⚖ 251 KB

The modern versions of the density functional theory DFT , especially those using the Ž . Ž . generalized gradient approximation GGA , have reached almost chemical accuracy and thus can be applied to study problems of real chemical interest such as catalysis. The Ž . important equations for the DFT,

Fast Photoisomerization of a Rhodopsin M

Fast Photoisomerization of a Rhodopsin Model—An Ab Initio Molecular Dynamics Study

✍ Volker Buß; Oliver Weingart; Minoru Sugihara 📂 Article 📅 2000 🏛 John Wiley and Sons 🌐 English ⚖ 119 KB 👁 1 views

Proton Transfer in Malonaldehyde: An Ab

Proton Transfer in Malonaldehyde: An Ab Initio Projector Augmented Wave Molecular Dynamics Study

✍ Katharina Wolf; Werner Mikenda; Ernst Nusterer; Karlheinz Schwarz; Claudia Ulbri 📂 Article 📅 1998 🏛 John Wiley and Sons 🌐 English ⚖ 319 KB 👁 1 views

Interconversion pathways of the protonat

Interconversion pathways of the protonated β-ionone Schiff base: An ab initio molecular dynamics study

✍ Frank Terstegen; Emily A. Carter; Volker Buss 📂 Article 📅 1999 🏛 John Wiley and Sons 🌐 English ⚖ 182 KB

Ab initio molecular dynamics at the RHFr3-21G level have been ## Ž . performed to study interconversion pathways bond rotation and ring inversion of the protonated ␤-ionone Schiff base. Starting with different stationary points on the Born᎐Oppenheimer potential energy surface, the trajectories ar

Ab initio Molecular Dynamics Simulations

Ab initio Molecular Dynamics Simulations of Reactions at Surfaces

✍ A. Gross 📂 Article 📅 2000 🏛 John Wiley and Sons 🌐 English ⚖ 395 KB 👁 1 views

Conformational Preferences for 3-Piperid

Conformational Preferences for 3-Piperideines: An Ab Initio and Molecular Mechanics Study

✍ Anatoly M. Belostotskii; Michael Shokhen; Hugo E. Gottlieb; Alfred Hassner 📂 Article 📅 2001 🏛 John Wiley and Sons 🌐 English ⚖ 205 KB 👁 1 views

Conformational preferences in alkyl-as well as Ph-substituted 3-piperideines (1,2,3,6-tetrahydropyridines) have been characterized by ab initio and molecular mechanics calculations. A set of rules and subrules for estimation of the conformational equilibrium (in terms of preferred substituent orient