FOLD-RATE: prediction of protein folding rates from amino acid sequence

Gromiha, M. Michael; Thangakani, A. Mary; Selvaraj, Samuel

doi:10.1093/nar/gkl043

Cited by 150 publications

(150 citation statements)

References 28 publications

Supporting

Mentioning

145

Contrasting

Unclassified

Order By: Relevance

“…Thus, inter-residue interactions have been one of the main focuses to understand the mechanisms of protein folding and stability [28][29][30][31][32][33][34]. Contact exploration in proteins could be of great interest from different perspectives, e.g.…”

Section: Introductionmentioning

confidence: 99%

Protein contacts, inter-residue interactions and side-chain modelling

Faure¹,

Bornot²,

Brevern³

2008

Biochimie

View full text Add to dashboard Cite

To cite this version:Guilhem Faure, Aurélie Bornot, Alexandre De Brevern. Protein contacts, inter-residue interactions and side-chain modelling.: protein contacts. Biochimie, Elsevier, 2008, 90 (4) AbstractThree-dimensional structures of proteins are the support of their biological functions.Their folds are stabilized by contacts between residues. Inner protein contacts are generally described through direct atomic contacts, i.e. interactions between side-chain atoms, while contact prediction methods mainly used inter-C distances. In this paper, we have analyzed the protein contacts on a recent high quality non-redundant databank using different criteria.First, we have studied the average number of contacts depending on the distance threshold to define a contact. Preferential contacts between types of amino acids have been highlighted.Detailed analyses have been done concerning the proximity of contacts in the sequence, the size of the proteins and fold classes. The strongest differences have been extracted, highlighting important residues.Then, we studied the influence of five different side-chain conformation prediction methods (SCWRL, IRECS, SCAP, SCATD and SSCOMP) on the distribution of contacts.The prediction rates of these different methods are quite similar. However, using a distance criterion between side-chains, the results are quite different, e.g. SCAP predicts 50% more contacts than observed, unlike other methods that predict fewer contacts than observed.Contacts deduced are quite distinct from one method to another with at most 75% contacts in common. Moreover, distributions of amino acid preferential contacts present unexpected behaviors distinct from previously observed in the X-ray structures, especially at the surface of proteins. For instance, the interactions involving Tryptophan greatly decrease.

show abstract

Section: Introductionmentioning

confidence: 99%

Protein contacts, inter-residue interactions and side-chain modelling

Faure¹,

Bornot²,

Brevern³

2008

Biochimie

View full text Add to dashboard Cite

show abstract

“…A variety of programs that predict the folding rate based on amino acid sequence integrated with other information have been published [8][9][10][11][12][13]. Recently, using Delaunay tessellation (DT) Ouyang and Liang [14] proposed a geometric contact (Nα) to replace the previous contact order.…”

mentioning

confidence: 99%

The dynamical contact order: Protein folding rate parameters based on quantum conformational transitions

Zhang

Luo

2011

Sci. China Life Sci.

View full text Add to dashboard Cite

Protein folding is regarded as a quantum transition between the torsion states of a polypeptide chain. According to the quantum theory of conformational dynamics, we propose the dynamical contact order (DCO) defined as a characteristic of the contact described by the moment of inertia and the torsion potential energy of the polypeptide chain between contact residues. Consequently, the protein folding rate can be quantitatively studied from the point of view of dynamics. By comparing theoretical calculations and experimental data on the folding rate of 80 proteins, we successfully validate the view that protein folding is a quantum conformational transition. We conclude that (i) a correlation between the protein folding rate and the contact inertial moment exists; (ii) multi-state protein folding can be regarded as a quantum conformational transition similar to that of two-state proteins but with an intermediate delay. We have estimated the order of magnitude of the time delay; (iii) folding can be classified into two types, exergonic and endergonic. Most of the two-state proteins with higher folding rate are exergonic and most of the multi-state proteins with low folding rate are endergonic. The folding speed limit is determined by exergonic folding. moment of inertia, dynamical contact order (DCO), protein folding rate Citation:Zhang Y, Luo L F. The dynamical contact order: Protein folding rate parameters based on quantum conformational transitions. Sci China Life Sci, 2011Sci, , 54: 386 -392, doi: 10.1007 Protein folding is a complex kinetic process by which a polypeptide changes from the denatured state to the native folding state. Although a great deal of theoretical work has been carried out, the fundamental physics underlying the folding remains unclear. The folding kinetics of a large number of proteins has been studied experimentally [1][2][3]. For many of these proteins, folding has been shown to be an all-or-none process with no clear intermediate state. These are called two-state proteins. However, some proteins require the accumulation of intermediates to complete the folding process. These are referred to as three-state or multi-state proteins. The rate of folding varies from milliseconds to hours. Some small proteins fold much faster, at rates in microsecond [2,3]. Experimental data has indicated that most of the ultrafast folders show a significant decrease in folding rates as the temperature is increased [4]. The wide range of folding rates and a possible folding speed limit are likely to be closely related to the inherent physics behind the phenomena. A deeper understanding of the folding mechanism and the accurate prediction of protein folding rates is an important topic in protein science. Since 1998, when the relative contact order (RCO) was proposed by Plaxco et al. [5], it has been widely accepted that folding rates and mechanisms are largely determined by the topology of the native state. Much theoretical work based on this concept has been proposed. For example, Ivankov et al. [6] pr...

show abstract

“…Plaxco and co-workers [119] showed that there is a high correlation between the folding rate and the structural properties of proteins, as defined by contact order CO, CO = 1 LN ∑ N ΔL ij , where L is the sequence length, N is the total number of inter-residue atomic contacts within a cutoff distance, ΔL ij is the sequence separation of contacting residues i and j. Interestingly, assessment of other protein folding rate determinants such as local and long-range contacts were found to perform equally well as the contact order [53]. Also, contact order is a geometric property which does not take into account the distribution and strength of the interactions on the rate [120].…”

Section: Protein Folding Kineticsmentioning

confidence: 98%

“…The Fold-Rate server (http://psfs.cbrc.jp/fold-rate/) [53] predicts rates of protein folding using the amino-acid sequence. The Parasol folding server (http://parasol.tamu.edu/groups/amatogroup/foldingserver) [54] predicts protein folding pathways using "probabilistic roadmaps"-based motion planning techniques.…”

Section: Studying Protein Foldingmentioning

confidence: 99%

Protein folding: Then and now

Chen

Ding

Nie

et al. 2008

Archives of Biochemistry and Biophysics

View full text Add to dashboard Cite

Over the past three decades the protein folding field has undergone monumental changes. Originally a purely academic question, how a protein folds has now become vital in understanding diseases and our abilities to rationally manipulate cellular life by engineering protein folding pathways. We review and contrast past and recent developments in the protein folding field. Specifically, we discuss the progress in our understanding of protein folding thermodynamics and kinetics, the properties of evasive intermediates, and unfolded states. We also discuss how some abnormalities in protein folding lead to protein aggregation and human diseases.

show abstract

FOLD-RATE: prediction of protein folding rates from amino acid sequence

Cited by 150 publications

References 28 publications

Protein contacts, inter-residue interactions and side-chain modelling

Protein contacts, inter-residue interactions and side-chain modelling

The dynamical contact order: Protein folding rate parameters based on quantum conformational transitions

Protein folding: Then and now

Contact Info

Product

Resources

About