Role of main-chain electrostatics, hydrophobic effect and side-chain conformational entropy in determining the secondary structure of proteins

Avbelj, Franc; Fele, Ljudmila

doi:10.1006/jmbi.1998.1792

Cited by 66 publications

(104 citation statements)

References 86 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Nearby side chains hinder access of solvent to the peptide group and reduce the negative ESF value. Consequently, helix and b-structure propensities of the different amino acids should depend on the ESF values of the peptide groups [100,[116][117][118]. The different helix propensities of the amino acids are often attributed instead to the loss in side-chain entropy when an unfolded peptide forms a helix [119].…”

Section: Prediction Of the Solvation Free Energies Of Peptide Groups mentioning

confidence: 99%

Weak Interactions in Protein Folding: Hydrophobic Free Energy, van der Waals Interactions, Peptide Hydrogen Bonds, and Peptide Solvation

Baldwin¹

2005

Protein Folding Handbook

View full text Add to dashboard Cite

Section: Prediction Of the Solvation Free Energies Of Peptide Groups mentioning

confidence: 99%

Weak Interactions in Protein Folding: Hydrophobic Free Energy, van der Waals Interactions, Peptide Hydrogen Bonds, and Peptide Solvation

Baldwin¹

2005

Protein Folding Handbook

View full text Add to dashboard Cite

“…, ρ C6H24 (12), ν C6C7 (7), ν C8C16 (6) 75 1612.1 37. 2 10.0 ν C13C15 (13), ν C10C11 (13), ν O5C9 (9), ν C12C13 (6), ν C8C19 (6), 3 β 3/R6 (5) 76 1615.0 82.5 6.3 ρ N3H23 (19), ν C6C19 (8), ν C8C19 (7), ν C16C18 (7), ν C10C11 (7), ν C7C18 (7), ν C13C15 (7), 1 β 2/R6 (5) 77 1627.4 34.0 15.0 ν C14C15 (14), ν C11C12 (11), ν O5C9 (8), 3 β 2/R6 (7), ν C12C13 (7), ν C6C7 (5) 78 1631.2 279.7 4.8 ν C6C7 (16), ν C8C19 (6), 1 β 3/R6 (6), ν C14C15 (6), ν O4C17 (6) (8), ω N3H23 (6) 7 162.7 0.4 0.3 4 bfl RR (14), τ N3C18 (10), 2 bfl RR (10), 1 (13), 4 bfl RR (10) 11 221.4 5.2 0.4 τ S1C20 (21), δ 2/C20H31H32 (12), 2 bfl RR (8), β C18N3C2 (7), 4 bfl RR (7) (14), ν C11C17 (10), δ 2/C20H31H32 (7), ν C9C16 (6) 17 425.5 10.2 0.3 3 τ 3/R6 (40), ρ C9O5 (12), 4 bfl RR (10), 3 (15), ν S1C20 (8), ρ C18N3 (6) 27 652.2 1.9 0.9 ν S1C20 (58), …”

mentioning

confidence: 99%

“…The component of the moment of inertia perpendicular to the molecular plane gives significant input to ΔS rot , whereas the largest contributions to the ΔS vib have the vibrations associated with the τ S1C20 coordinate. The hydrophobic effect, side-chain conformational entropy, steric factors, and main-chain electrostatic interactions have been indicated as the dominant physical factors that determine conformational preferences of amino acids in proteins [12]. In particular, it has been demonstrated that restriction of amino acids side-chain motion is enthalpically favorable, but unfavorable in terms of Gibbs energy and entropy [13].…”

mentioning

confidence: 99%

“…In accordance to that, vibrations associated with the τ S1C20 coordinate has the greatest impact on vibrational entropy differences ( (9), ν C10C11 (7), ν S1C20 (6) (9), ω C13H27 (7), ω C15H29 (6), ω C7H25 (6) (14), ω C12H26 (14), ω C14H28 (13), ω C7H25 (7) 47 1013.7 85.1 2.0 ν C8C17 (12), ν C2C20 (8), ν C2N3 (7), ν C11C12 (6), ρ C2H22H21 (6), ν C13C15 (5) 48 (12), ν C6C7 (7) 52 1113.2 1.0 0. (12), τ C2H22H21 (10), ν C7C18 (10), ρ C12H26 (8), τ C20H31H32 (7), ρ C7H25 (6) 60 1271.6 41.6 0.7 (5) 63 1325.9 149.6 6.8 (5) 65 1358.7 25.7 1.0 ν C10C14 (14), ν C11C12 (14), ν C10C11 (14), ν C13C15 (13), ν C12C13 (13), ν C14C15 (12) 66 1381.0 12.6 1.7 ν C16C18 (15), ν C8C16 (13), ν C8C19 (12), ν C6C19 (7), ν C9C16 (6), ν C6C7 (6), ν C7C18 (5), ρ C9O5 (5) (14), β C18N3C2 (12), τ S1C20 (10), ν C16C18 (6) 14 323.5 2.1 0.5 τ S1C20 (13), δ 2/C2H22H21 (12), δ 2/C20H31H32 (11), τ C2C20 (10), β C18N3C2 (8), τ C2N3 (7), ρ C17O4 (6) (9), ρ C14H28 (9), ν C14C15 (9), ν C12C13 (7), ρ C20H31H32 (7), ρ C2H22H21 (6) (14), ν C6C7 …”

mentioning

confidence: 99%

“…1.6 ρ C20H31H32 (25), β C20S1H33 (14), 1 β 3/R6 (8), 1 β trig/R6 (5) 35 785.9 5.5 0.3 3 τ 1/R6 (18), 2 τ 1/R6 (13), ω C7H25 (12), ω C9O5 (10), ω C19H30 (10), ω C17O4 (9), ω C6H24 (9) 36 796.0 0.1 0.7 1 β trig/R6 (13), ρ C20H31H32 (12), β C20S1H33 (12), 3 β 2/R6 (10), 1 β 3/R6 (9), 3 β trig/R6 (7) 37 808.4 0.5 0.1 ω C9O5 (25), ω C13H27 (13) (12), ν C8C19 (10), ν C11C17 (7), ρ C6H24 (6), ρ C14H28 (6) 58 1221.4 39.6 0.5 τ C20H31H32 (51), τ C2H22H21 (10) 59 1256. (7) 61 1293.8 528.9 10.6 (5) 62 1317.6 120.0 1.…”

mentioning

confidence: 99%

See 2 more Smart Citations

Relationship between structure and entropy contributions in an anthraquinone mercapto derivative

2010

View full text Add to dashboard Cite

The structural and thermodynamic properties of an anthraquinone derivative were studied by means of quantum-chemical calculations. As a result of the conformational analysis fourteen lowenergetic conformers were found by using ab initio and DFT methods. In order to discuss similarities and differences in entropy of the conformers, the rotational and vibrational contributions to entropy were correlated with changes in the conformer structure. The moment of inertia perpendicular to the molecular plane gives significant input to the ΔSrot, whereas the largest contributions to the ΔSvib have the vibrations associated with the τS1C20 coordinate.Response to Reviewers: Dear Prof. Andrzej Sokalski Editor in Chief of Journal of Molecular Modeling, I would like to thank the Referees for a careful reading of our manuscript and giving us the valuable comments that with no doubts will improve this paper (Mns.# JMMO1081). Please find below my answers to the Referees' suggestions and comments.Reviewer #1:Major Revisions 1. Some anthraquinones are proved to have anti-cancer and antifungal properties, as stated by the authors in the introduction. There, the anthraquinones are not in gas phase, but solved in the liquid phase or are interacting with the target in the liquid phase. In contrast, the calculations of the authors are performed in the gas phase. Thus, the authors should discuss, if their results have significance in drug research and for interaction between ligand and target. The molecular structure defined in the gas phase is a commonly accepted starting point in studies concerning biological activities of molecules. Indeed, we agree with the referee that the future research dealing strictly with biological activity of anthraquinones would require introduction of the solvent and simulation of a biological environment in computational models that is, by the way, a nontrivial problem. However, our studies on antraquinones brought us to finding of the entropic effect in the structures of the MEAA conformers and we decided to analyze this effect in detail. Therefore, our work, although mentioning biological functions of MEAA conformers, was in fact aimed to study the correlation of the rotational and vibrational contributions to entropy with changes in the conformer structure and to do this, the simplest possible model (the gas phase) occurred to us as the most preferable. In order to clarify our point of view we suggest adding two more sentences to Introduction (after : The highest emphasis was made on detailed analysis of the entropy effect in order to understand the relation between the structure and entropy contributions (translational, electronic, rotational and vibrational). The computations were done in the gas phase to simplify the computations. Nevertheless, it is hoped that this study can be a starting point in the future research concerning modeling of the biological activity of the MEAA in more complicated systems, mimicking the biological environment.2. How was the analysis of the potential energy p...

show abstract

Prediction of the three-dimensional structure of proteins using the electrostatic screening model and hierarchic condensation

Avbelj

Fele

1998

Proteins

View full text Add to dashboard Cite

We describe a method for predicting the three-dimensional (3-D) structure of proteins from their sequence alone. The method is based on the electrostatic screening model for the stability of the protein main-chain conformation. The free energy of a protein as a function of its conformation is obtained from the potentials of mean force analysis of high-resolution x-ray protein structures. The free energy function is simple and contains only 44 fitted coefficients. The minimization of the free energy is performed by the torsion space Monte Carlo procedure using the concept of hierarchic condensation. The Monte Carlo minimization procedure is applied to predict the secondary, super-secondary, and native 3-D structures of 12 proteins with 28-110 amino acids. The 3-D structures of the majority of local secondary and super-secondary structures are predicted accurately. This result suggests that control in forming the native-like local structure is distributed along the entire protein sequence. The native 3-D structure is predicted correctly for 3 of 12 proteins composed mainly from the alpha-helices. The method fails to predict the native 3-D structure of proteins with a predominantly beta secondary structure. We suggest that the hierarchic condensation is not an appropriate procedure for simulating the folding of proteins made up primarily from beta-strands. The method has been proved accurate in predicting the local secondary and super-secondary structures in the blind ab initio 3-D prediction experiment.

show abstract

Role of main-chain electrostatics, hydrophobic effect and side-chain conformational entropy in determining the secondary structure of proteins

Cited by 66 publications

References 86 publications

Weak Interactions in Protein Folding: Hydrophobic Free Energy, van der Waals Interactions, Peptide Hydrogen Bonds, and Peptide Solvation

Weak Interactions in Protein Folding: Hydrophobic Free Energy, van der Waals Interactions, Peptide Hydrogen Bonds, and Peptide Solvation

Relationship between structure and entropy contributions in an anthraquinone mercapto derivative

Prediction of the three-dimensional structure of proteins using the electrostatic screening model and hierarchic condensation

Contact Info

Product

Resources

About