TITLE

Comparison of molecular dynamics and superfamily spaces of protein domain deformation

AUTHOR(S)
Velázquez-Muriel, Javier A.; Rueda, Manuel; Cuesta, Isabel; Pascual-Montano, Alberto; Orozco, Modesto; Carazo, José-María
PUB. DATE
January 2009
SOURCE
BMC Structural Biology;2009, Vol. 9, Special section p1
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Background: It is well known the strong relationship between protein structure and flexibility, on one hand, and biological protein function, on the other hand. Technically, protein flexibility exploration is an essential task in many applications, such as protein structure prediction and modeling. In this contribution we have compared two different approaches to explore the flexibility space of protein domains: i) molecular dynamics (MD-space), and ii) the study of the structural changes within superfamily (SF-space). Results: Our analysis indicates that the MD-space and the SF-space display a significant overlap, but are still different enough to be considered as complementary. The SF-space space is wider but less complex than the MD-space, irrespective of the number of members in the superfamily. Also, the SF-space does not sample all possibilities offered by the MD-space, but often introduces very large changes along just a few deformation modes, whose number tend to a plateau as the number of related folds in the superfamily increases. Conclusion: Theoretically, we obtained two conclusions. First, that function restricts the access to some flexibility patterns to evolution, as we observe that when a superfamily member changes to become another, the path does not completely overlap with the physical deformability. Second, that conformational changes from variation in a superfamily are larger and much simpler than those allowed by physical deformability. Methodologically, the conclusion is that both spaces studied are complementary, and have different size and complexity. We expect this fact to have application in fields as 3D-EM/X-ray hybrid models or ab initio protein folding.
ACCESSION #
42634743

 

Related Articles

  • Molecular dynamics of folding of secondary structures in Go-type models of proteins. Hoang, Trinh Xuan; Trinh Xuan Hoang; Cieplak, Marek // Journal of Chemical Physics;4/15/2000, Vol. 112 Issue 15 

    We consider six different secondary structures of proteins and construct two types of Go-type off-lattice models: with the steric constraints and without. The basic amino acid-amino acid potential is Lennard-Jones for the native contacts and a soft repulsion for the non-native contacts. The...

  • Absolute comparison of simulated and experimental protein-folding dynamics. Snow, Christopher D.; Nguyen, Houbi; Pande, Vijay S.; Gruebele, Martin // Nature;11/7/2002, Vol. 420 Issue 6911, p102 

    Protein folding is difficult to simulate with classical molecular dynamics. Secondary structure motifs such as α-helices and βhairpins can form in 0.1-10 µs (ref. 1), whereas small proteins have been shown to fold completely in tens of microseconds. The longest folding simulation to...

  • An intermediate seeks instant gratification. Gruebele, Martin // Nature Structural Biology;Mar2002, Vol. 9 Issue 3, p154 

    Focuses on a φ-value analysis of the four-helix protein Im7 which reveals that a folding intermediate with non-native structure rapidly forms en route to the native state. Factors influencing the folding dynamics; General kinetic equations connecting three states; Range of φ values...

  • Physics and biophysics of solvent induced forces: hydrophobic interactions and context-dependent hydration. San Biagio, P. L.; Bulone, D.; Martorana, V.; Palma-Vittorelli, M. B.; Palma, M. U. // European Biophysics Journal;1998, Vol. 27 Issue 3, p183 

    Solvent induced forces (SIFs) among solutes derive from solvent structural modification due to solutes, and consequent thermodynamic drive towards minimization of related free energy costs. The role of SIFs in biomolecular conformation and function is appreciated by observing that typical SIF...

  • Theory for the rate of contact formation in a polymer chain with local conformational transitions. Zhou, Huan-Xiang // Journal of Chemical Physics;1/22/2003, Vol. 118 Issue 4, p2010 

    I derive an expression for the rate of contact formation between two residues in a polymer chain when both residues undergo native to non-native conformational transitions. A contact can only form when the two residues are brought into contact by interresidue diffusion and are in the native...

  • Brownian dynamics simulations of protein folding. Siqian He; Scheraga, Harold A. // Journal of Chemical Physics;1/1/1998, Vol. 108 Issue 1, p287 

    Analyzes protein folding mechanism and kinetics through torsional angle space macromolecular dynamics treatment. Determination of torsional angle space algorithm; Description of conformational functions; Role of hydrophobic collapse in the folding processes; Introduction of global dipole...

  • Characterisation of transition state structures for protein folding using high, medium and low {Phi}-values. Christian D. Geierhaas; Xavier Salvatella; Jane Clarke; Michele Vendruscolo // PEDS: Protein Engineering, Design & Selection;Mar2008, Vol. 21 Issue 3, p215 

    It has been suggested that Φ-values, which allow structural information about transition states (TSs) for protein folding to be obtained, are most reliably interpreted when divided into three classes (high, medium and low). High Φ-values indicate almost completely folded regions in the TS,...

  • The role of sidechain packing and native contact interactions in folding: Discontinuous molecular dynamics folding simulations of an all-atom Gō model of fragment B of Staphylococcal protein A. Linhananta, Apichart; Zhou, Yaoqi // Journal of Chemical Physics;11/15/2002, Vol. 117 Issue 19, p8983 

    Protein topology, which refers to the arrangement of secondary structures of proteins, has been extensively investigated to examine its role in protein folding. However, recent studies show that topology alone cannot account for the variation of folding behaviors observed in some proteins of the...

  • Does folding determine protein configuration? Maddox, John // Nature;7/7/1994, Vol. 370 Issue 6484, p13 

    Discusses a concept for addressing the problem of protein folding. Arbitrary selection of the configuration of a notional protein; Use of conventional molecular dynamics; Novelty of the concept.

Share

Read the Article

Courtesy of THE LIBRARY OF VIRGINIA

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics