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Literature DB >> 22089251

Understanding biomolecular motion, recognition, and allostery by use of conformational ensembles.

R Bryn Fenwick¹, Santi Esteban-Martín, Xavier Salvatella.

Abstract

We review the role conformational ensembles can play in the analysis of biomolecular dynamics, molecular recognition, and allostery. We introduce currently available methods for generating ensembles of biomolecules and illustrate their application with relevant examples from the literature. We show how, for binding, conformational ensembles provide a way of distinguishing the competing models of induced fit and conformational selection. For allostery we review the classic models and show how conformational ensembles can play a role in unravelling the intricate pathways of communication that enable allostery to occur. Finally, we discuss the limitations of conformational ensembles and highlight some potential applications for the future.

Entities: Chemical Disease Gene Species

Mesh：

Substances：
Proteins
RNA
DNA

Year: 2011 PMID： 22089251 PMCID： PMC3222826 DOI： 10.1007/s00249-011-0754-8

Source DB: PubMed Journal: Eur Biophys J ISSN： 0175-7571 Impact factor: 1.733

136 in total

Review 1. Folding funnels, binding funnels, and protein function.

Authors: C J Tsai; S Kumar; B Ma; R Nussinov
Journal: Protein Sci Date: 1999-06 Impact factor: 6.725

2. Analysis of correlated motion in antibody combining sites from molecular dynamics simulations.

Authors: M Viswanathan; D S Linthicum; S Subramaniam
Journal: Methods Date: 2000-03 Impact factor: 3.608

3. Orientation restraints in molecular dynamics simulations using time and ensemble averaging.

Authors: B Hess; R M Scheek
Journal: J Magn Reson Date: 2003-09 Impact factor: 2.229

4. STRUCTURE OF HAEMOGLOBIN. A THREE-DIMENSIONAL FOURIER SYNTHESIS OF REDUCED HUMAN HAEMOGLOBIN AT 5-5 A RESOLUTION.

Authors: H MUIRHEAD; M F PERUTZ
Journal: Nature Date: 1963-08-17 Impact factor: 49.962

5. Free energy surfaces from single-distance information.

Authors: Philipp Schuetz; René Wuttke; Benjamin Schuler; Amedeo Caflisch
Journal: J Phys Chem B Date: 2010-10-22 Impact factor: 2.991

6. A unified model of protein dynamics.

Authors: Hans Frauenfelder; Guo Chen; Joel Berendzen; Paul W Fenimore; Helén Jansson; Benjamin H McMahon; Izabela R Stroe; Jan Swenson; Robert D Young
Journal: Proc Natl Acad Sci U S A Date: 2009-02-27 Impact factor: 11.205

7. Dynamic energy landscape view of coupled binding and protein conformational change: induced-fit versus population-shift mechanisms.

Authors: Kei-Ichi Okazaki; Shoji Takada
Journal: Proc Natl Acad Sci U S A Date: 2008-08-04 Impact factor: 11.205

8. Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin.

Authors: Tomasz Wlodarski; Bojan Zagrovic
Journal: Proc Natl Acad Sci U S A Date: 2009-11-03 Impact factor: 11.205

9. New insight into long-range nonadditivity within protein double-mutant cycles.

Authors: Andrei Y Istomin; M Michael Gromiha; Oleg K Vorov; Donald J Jacobs; Dennis R Livesay
Journal: Proteins Date: 2008-02-15

10. Coupling interactions of distal residues enhance dihydrofolate reductase catalysis: mutational effects on hydride transfer rates.

Authors: P T Ravi Rajagopalan; Stefan Lutz; Stephen J Benkovic
Journal: Biochemistry Date: 2002-10-22 Impact factor: 3.162

34 in total

Understanding biomolecular motion, recognition, and allostery by use of conformational ensembles.

Review 1. Folding funnels, binding funnels, and protein function.

2. Analysis of correlated motion in antibody combining sites from molecular dynamics simulations.

3. Orientation restraints in molecular dynamics simulations using time and ensemble averaging.

4. STRUCTURE OF HAEMOGLOBIN. A THREE-DIMENSIONAL FOURIER SYNTHESIS OF REDUCED HUMAN HAEMOGLOBIN AT 5-5 A RESOLUTION.

5. Free energy surfaces from single-distance information.

6. A unified model of protein dynamics.

7. Dynamic energy landscape view of coupled binding and protein conformational change: induced-fit versus population-shift mechanisms.

8. Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin.

9. New insight into long-range nonadditivity within protein double-mutant cycles.

10. Coupling interactions of distal residues enhance dihydrofolate reductase catalysis: mutational effects on hydride transfer rates.

1. The Exact NOE as an Alternative in Ensemble Structure Determination.

2. Extending the eNOE data set of large proteins by evaluation of NOEs with unresolved diagonals.

3. Visualizing correlated motion with HDBSCAN clustering.

4. Paradoxes and wonders of intrinsic disorder: Complexity of simplicity.

Review 5. Conditionally disordered proteins: bringing the environment back into the fold.

6. Structural and Dynamic Insights of the Interaction between Tritrpticin and Micelles: An NMR Study.

7. Dynamical persistence of active sites identified in maltose-binding protein.

8. Direct Investigation of Slow Correlated Dynamics in Proteins via Dipolar Interactions.

9. Multiple pathways promote dynamical coupling between catalytic domains in Escherichia coli prolyl-tRNA synthetase.

Review 10. Computational approaches to mapping allosteric pathways.