Empirical solvent‐mediated potentials hold for both intra‐molecular and inter‐molecular inter‐residue interactions

Keskin, Özlem; Bahar, İvet; Badretdinov, Azat Ya.; Ptitsyn, Oleg B.; Jernigan, Robert L.

doi:10.1002/pro.5560071211

Cited by 90 publications

(104 citation statements)

References 26 publications

(20 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…These values were already successfully used with the SCPCP method on a more coarse-grained level in the study of binding of bovine pancreatic phospholipase A2 [27]. The interactions between different proteins were weighted according to the values reported in [28]. The intra-RNA contacts were assigned a strength of 2.51RT, the protein-RNA interactions an energy of 2.83RT [9,29,30].…”

Section: Methodsmentioning

confidence: 99%

Dependency Map of Proteins in the Small Ribosomal Subunit

Hamacher¹,

Trylska²,

McCammon³

2005

PLoS Comp Biol

View full text Add to dashboard Cite

The assembly of the ribosome has recently become an interesting target for antibiotics in several bacteria. In this work, we extended an analytical procedure to determine native state fluctuations and contact breaking to investigate the protein stability dependence in the 30S small ribosomal subunit of Thermus thermophilus. We determined the causal influence of the presence and absence of proteins in the 30S complex on the binding free energies of other proteins. The predicted dependencies are in overall agreement with the experimentally determined assembly map for another organism, Escherichia coli. We found that the causal influences result from two distinct mechanisms: one is pure internal energy change, the other originates from the entropy change. We discuss the implications on how to target the ribosomal assembly most effectively by suggesting six proteins as targets for mutations or other hindering of their binding. Our results show that by blocking one out of this set of proteins, the association of other proteins is eventually reduced, thus reducing the translation efficiency even more. We could additionally determine the binding dependency of THX-a peptide not present in the ribosome of E. coli-and suggest its assembly path.

show abstract

Section: Methodsmentioning

confidence: 99%

Dependency Map of Proteins in the Small Ribosomal Subunit

Hamacher¹,

Trylska²,

McCammon³

2005

PLoS Comp Biol

View full text Add to dashboard Cite

show abstract

“…The interaction between a proline ring and an aromatic ring resembles the interaction between two aromatic rings [9], and this can be seen in the higher preference for the Pro-Trp (P-W) pair. Keskin et al [12] investigated the residue contacts at protein-protein interfaces using ''solvent-mediated'' potentials and ''residuemediated'' potentials. The abundance of the Cys-Cys contact, hydrophobic contacts, and aromatic contacts in interfaces observed in this study are consistent with the low values of the residue-mediated potentials for these contacts reported by Keskin et al [12].…”

Section: Secondary Structure-mentioning

confidence: 99%

“…Keskin et al [12] investigated the residue contacts at protein-protein interfaces using ''solvent-mediated'' potentials and ''residuemediated'' potentials. The abundance of the Cys-Cys contact, hydrophobic contacts, and aromatic contacts in interfaces observed in this study are consistent with the low values of the residue-mediated potentials for these contacts reported by Keskin et al [12].…”

Section: Secondary Structure-mentioning

confidence: 99%

“…Miyazawa and Jernigan [11] developed a method to extract inter-residue potentials from frequencies of contacts between different residues in proteins. Later, Keskin et al [12] showed that the potentials of mean force for inter-residue interactions hold for both intra-molecular and inter-molecular interactions. The important role of hydrophobic forces in protein-protein interactions has been confirmed by several researchers [13,14].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Characterization of Protein–Protein Interfaces

et al. 2007

View full text Add to dashboard Cite

We analyze the characteristics of protein-protein interfaces using the largest datasets available from the Protein Data Bank (PDB). We start with a comparison of interfaces with protein cores and noninterface surfaces. The results show that interfaces differ from protein cores and non-interface surfaces in residue composition, sequence entropy, and secondary structure. Since interfaces, protein cores, and non-interface surfaces have different solvent accessibilities, it is important to investigate whether the observed differences are due to the differences in solvent accessibility or differences in functionality. We separate out the effect of solvent accessibility by comparing interfaces with a set of residues having the same solvent accessibility as the interfaces. This strategy reveals residue distribution propensities that are not observable by comparing interfaces with protein cores and noninterface surfaces. Our conclusions are that there are larger numbers of hydrophobic residues, particularly aromatic residues, in interfaces, and the interactions apparently favored in interfaces include the opposite charge pairs and hydrophobic pairs. Surprisingly, Pro-Trp pairs are over represented in interfaces, presumably because of favorable geometries. The analysis is repeated using three datasets having different constraints on sequence similarity and structure quality. Consistent results are obtained across these datasets. We have also investigated separately the characteristics of heteromeric interfaces and homomeric interfaces.

show abstract

“…Each u and w angle is divided into intervals of 308; thus, 12 representative torsion states are assigned to each bond. [41][42][43] The statis-tics for the u i w i and w i u i þ1 pairs could as well be obtained from pairs of residues, YZ without incorporating the i À 1th residue, X, along the sequence. This would improve the statistics in the nonredundant database significantly.…”

Section: Determination Of the Initial Conformationsmentioning

confidence: 99%

Relationships between unfolded configurations of proteins and dynamics of folding to the native state

Gürsoy

Keskin

Türkay

et al. 2006

J Polym Sci B Polym Phys

View full text Add to dashboard Cite

ABSTRACT:We compare folding trajectories of chymotrypsin inhibitor (CI2) using a dynamic Monte Carlo scheme with Go-type potentials. The model considers the four backbone atoms of each residue and a sphere centered around C b the diameter of which is chosen according to the type of the side group. Bond lengths and bond angles are kept fixed. Folding trajectories are obtained by giving random increments to the u and w torsion angles with some bias toward the native state. Excluded volume effects are considered. Two sets of 20 trajectories are obtained, with different initial configurations. The first set is generated from random initial configurations. The initial configurations of the second set are generated according to knowledge-based neighbor dependent torsion probabilities derived from triplets in the Protein Data Bank. Compared to chains with randomly generated initial configurations, those generated with neighbor-dependent probabilities (i) fold faster, (ii) have better defined secondary structure elements, and (iii) have less number of non-native contacts during folding.

show abstract

Empirical solvent‐mediated potentials hold for both intra‐molecular and inter‐molecular inter‐residue interactions

Cited by 90 publications

References 26 publications

Dependency Map of Proteins in the Small Ribosomal Subunit

Dependency Map of Proteins in the Small Ribosomal Subunit

Characterization of Protein–Protein Interfaces

Relationships between unfolded configurations of proteins and dynamics of folding to the native state

Contact Info

Product

Resources

About