Literature DB >> 15772308

The flexibility in the proline ring couples to the protein backbone.

Bosco K Ho1, Evangelos A Coutsias, Chaok Seok, Ken A Dill.   

Abstract

In proteins, the proline ring exists predominantly in two discrete states. However, there is also a small but significant amount of flexibility in the proline ring of high-resolution protein structures. We have found that this side-chain flexibility is coupled to the backbone conformation. To study this coupling, we have developed a model that is simply based on geometric and steric factors and not on energetics. We show that the coupling between phi and chi1 torsions in the proline ring can be described by an analytic equation that was developed by Bricard in 1897, and we describe a computer algorithm that implements the equation. The model predicts the observed coupling very well. The strain in the C(gamma)-C(delta)-N angle appears to be the principal barrier between the UP and DOWN pucker. This strain is relaxed to allow the proline ring to flatten in the rare PLANAR conformation.

Entities:  

Mesh:

Substances:

Year:  2005        PMID: 15772308      PMCID: PMC2253451          DOI: 10.1110/ps.041156905

Source DB:  PubMed          Journal:  Protein Sci        ISSN: 0961-8368            Impact factor:   6.725


  16 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  Cis peptide bonds in proteins: residues involved, their conformations, interactions and locations.

Authors:  D Pal; P Chakrabarti
Journal:  J Mol Biol       Date:  1999-11-19       Impact factor: 5.469

3.  Revisiting the Ramachandran plot: hard-sphere repulsion, electrostatics, and H-bonding in the alpha-helix.

Authors:  Bosco K Ho; Annick Thomas; Robert Brasseur
Journal:  Protein Sci       Date:  2003-11       Impact factor: 6.725

4.  A kinematic view of loop closure.

Authors:  Evangelos A Coutsias; Chaok Seok; Matthew P Jacobson; Ken A Dill
Journal:  J Comput Chem       Date:  2004-03       Impact factor: 3.376

5.  Structure validation by Calpha geometry: phi,psi and Cbeta deviation.

Authors:  Simon C Lovell; Ian W Davis; W Bryan Arendall; Paul I W de Bakker; J Michael Word; Michael G Prisant; Jane S Richardson; David C Richardson
Journal:  Proteins       Date:  2003-02-15

6.  Modeling of globular proteins. A distance-based data search procedure for the construction of insertion/deletion regions and Pro----non-Pro mutations.

Authors:  N L Summers; M Karplus
Journal:  J Mol Biol       Date:  1990-12-20       Impact factor: 5.469

7.  Who checks the checkers? Four validation tools applied to eight atomic resolution structures. EU 3-D Validation Network.

Authors: 
Journal:  J Mol Biol       Date:  1998-02-20       Impact factor: 5.469

8.  Studies on the conformation of amino acids. XII. Energy calculations on prolyl residue.

Authors:  G N Ramachandran; A V Lakshminarayanan; R Balasubramanian; G Tegoni
Journal:  Biochim Biophys Acta       Date:  1970-11-17

9.  Conformations of proline.

Authors:  D F De Tar; N P Luthra
Journal:  J Am Chem Soc       Date:  1977-02-16       Impact factor: 15.419

10.  All-atom empirical potential for molecular modeling and dynamics studies of proteins.

Authors:  A D MacKerell; D Bashford; M Bellott; R L Dunbrack; J D Evanseck; M J Field; S Fischer; J Gao; H Guo; S Ha; D Joseph-McCarthy; L Kuchnir; K Kuczera; F T Lau; C Mattos; S Michnick; T Ngo; D T Nguyen; B Prodhom; W E Reiher; B Roux; M Schlenkrich; J C Smith; R Stote; J Straub; M Watanabe; J Wiórkiewicz-Kuczera; D Yin; M Karplus
Journal:  J Phys Chem B       Date:  1998-04-30       Impact factor: 2.991

View more
  28 in total

1.  Exploring the energy landscapes of protein folding simulations with Bayesian computation.

Authors:  Nikolas S Burkoff; Csilla Várnai; Stephen A Wells; David L Wild
Journal:  Biophys J       Date:  2012-02-21       Impact factor: 4.033

2.  Exhaustive Conformational Sampling of Complex Fused Ring Macrocycles Using Inverse Kinematics.

Authors:  Evangelos A Coutsias; Katrina W Lexa; Michael J Wester; Sara N Pollock; Matthew P Jacobson
Journal:  J Chem Theory Comput       Date:  2016-08-04       Impact factor: 6.006

3.  Dead-end elimination with perturbations (DEEPer): a provable protein design algorithm with continuous sidechain and backbone flexibility.

Authors:  Mark A Hallen; Daniel A Keedy; Bruce R Donald
Journal:  Proteins       Date:  2012-09-18

4.  Methods for Monte Carlo simulations of biomacromolecules.

Authors:  Andreas Vitalis; Rohit V Pappu
Journal:  Annu Rep Comput Chem       Date:  2009-01-01

5.  Residue-centric modeling and design of saccharide and glycoconjugate structures.

Authors:  Jason W Labonte; Jared Adolf-Bryfogle; William R Schief; Jeffrey J Gray
Journal:  J Comput Chem       Date:  2016-11-30       Impact factor: 3.376

6.  Competing noncovalent host-guest interactions and H/D exchange: reactions of benzyloxycarbonyl-proline glycine dipeptide variants with ND3.

Authors:  Mahsan Miladi; Abayomi D Olaitan; Behrooz Zekavat; Touradj Solouki
Journal:  J Am Soc Mass Spectrom       Date:  2015-08-21       Impact factor: 3.109

7.  On the evolutionary significance of the size and planarity of the proline ring.

Authors:  Jörn Behre; Roland Voigt; Ingo Althöfer; Stefan Schuster
Journal:  Naturwissenschaften       Date:  2012-09-15

8.  The mechanism of domain alternation in the acyl-adenylate forming ligase superfamily member 4-chlorobenzoate: coenzyme A ligase.

Authors:  Rui Wu; Albert S Reger; Xuefeng Lu; Andrew M Gulick; Debra Dunaway-Mariano
Journal:  Biochemistry       Date:  2009-05-19       Impact factor: 3.162

9.  The mechanism of ubiquitination in the cullin-RING E3 ligase machinery: conformational control of substrate orientation.

Authors:  Jin Liu; Ruth Nussinov
Journal:  PLoS Comput Biol       Date:  2009-10-02       Impact factor: 4.475

10.  Mechanism of action of cyclophilin a explored by metadynamics simulations.

Authors:  Vanessa Leone; Gianluca Lattanzi; Carla Molteni; Paolo Carloni
Journal:  PLoS Comput Biol       Date:  2009-03-13       Impact factor: 4.475

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.