Differential geometry and polymer conformation. 3. Single-site and nearest-neighbor distribution and nucleation of protein folding

1981 ◽  
Vol 14 (5) ◽  
pp. 1259-1269 ◽  
Author(s):  
S. Rackovsky ◽  
H. A. Scheraga
Keyword(s):  
Differential Geometry ◽  
Protein Folding ◽  
Nearest Neighbor ◽  
Single Site ◽  
Polymer Conformation

Differential geometry and protein folding

1984 ◽  
Vol 17 (6) ◽  
pp. 209-214 ◽  
Author(s):  
S. Rackovsky ◽  
H. A. Scheraga
Keyword(s):  
Differential Geometry ◽  
Protein Folding

Analysis of Tandem Repeat Protein Folding Using Nearest-Neighbor Models

2021 ◽  
Vol 50 (1) ◽  
Author(s):  
Mark Petersen ◽  
Doug Barrick
Keyword(s):  
Protein Folding ◽  
Tandem Repeat ◽  
Nearest Neighbor ◽  
Experimental System ◽  
Structural Features ◽  
Internal Symmetry ◽  
Statistical Thermodynamic ◽  
Annual Review ◽  
Publication Date ◽  
Repeat Proteins

Cooperativity is a hallmark of protein folding, but the thermodynamic origins of cooperativity are difficult to quantify. Tandem repeat proteins provide a unique experimental system to quantify cooperativity due to their internal symmetry and their tolerance of deletion, extension, and in some cases fragmentation into single repeats. Analysis of repeat proteins of different lengths with nearest-neighbor Ising models provides values for repeat folding (ΔGi) and inter-repeat coupling (Δ Gi-1, i). In this article, we review the architecture of repeat proteins and classify them in terms of Δ Gi and Δ Gi-1, i; this classification scheme groups repeat proteins according to their degree of cooperativity. We then present various statistical thermodynamic models, based on the 1D-Ising model, for analysis of different classes of repeat proteins. We use these models to analyze data for highly and moderately cooperative and noncooperative repeat proteins and relate their fitted parameters to overall structural features. Expected final online publication date for the Annual Review of Biophysics, Volume 50 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals On the Role of Entropy in the Stabilization of α-Helixes

2020 ◽  
Author(s):  
Adolfo Bastida ◽  
José Zúñiga ◽  
Alberto Requena ◽  
Beatriz Miguel ◽  
Javier Cerezo
Keyword(s):  
Free Energy ◽  
Protein Folding ◽  
Nearest Neighbor ◽  
Conformational Space ◽  
Folded Structure ◽  
Enthalpy And Entropy Changes ◽  
Potential Energy Landscapes ◽  
Folded Structures ◽  
Dynamics Simulations

Protein folding evolves by exploring the conformational space with a subtle balance between enthalpy and entropy changes which eventually leads to a decrease of the free energy upon reaching the folded structure. <br>A complete understanding of this process requires, therefore, a deep insight into both contributions to the free energy.<br>In this work, we clarify the role of entropy in favoring the stabilization of folded structures in polyalanine peptides with up to 12 residues . We use a novel method referred to as K2V that allows us to obtain the potential energy landscapes in terms of residue conformations extracted from molecular dynamics simulations at conformational equilibrium, and yields folding thermodynamic magnitudes in agreement with the experimental data available. <br>Our results demonstrate that the folded structures of the larger polyalanine chains are stabilized with respect to the folded structures of the shorter chains mostly by an increase of the entropic contribution of the solvent, which compensates the decrease of conformational entropy of the polypeptide, thus unveiling a key piece in the puzzle of protein folding.<br>In addition, the ability of the K2V method to provide the enthalpic and entropic contributions for individual residues along the peptide chain makes it clear that the entropic stabilization is basically governed by the nearest neighbor residues conformations, with the folding propensity being rationalized in terms of triads of residues.<br><br>

Minimalist Representations and the Importance of Nearest Neighbor Effects in Protein Folding Simulations

2006 ◽  
Vol 363 (4) ◽  
pp. 835-857 ◽  
Author(s):  
Andrés Colubri ◽  
Abhishek K. Jha ◽  
Min-yi Shen ◽  
Andrej Sali ◽  
R. Stephen Berry ◽  
...  
Keyword(s):  
Protein Folding ◽  
Nearest Neighbor ◽  
Neighbor Effects ◽  
Folding Simulations

scholarly journals On the Role of Entropy in the Stabilization of α-Helixes

2020 ◽  
Author(s):  
Adolfo Bastida ◽  
José Zúñiga ◽  
Alberto Requena ◽  
Beatriz Miguel ◽  
Javier Cerezo
Keyword(s):  
Free Energy ◽  
Protein Folding ◽  
Nearest Neighbor ◽  
Conformational Space ◽  
Folded Structure ◽  
Enthalpy And Entropy Changes ◽  
Potential Energy Landscapes ◽  
Folded Structures ◽  
Dynamics Simulations

Protein folding evolves by exploring the conformational space with a subtle balance between enthalpy and entropy changes which eventually leads to a decrease of the free energy upon reaching the folded structure. <br>A complete understanding of this process requires, therefore, a deep insight into both contributions to the free energy.<br>In this work, we clarify the role of entropy in favoring the stabilization of folded structures in polyalanine peptides with up to 12 residues . We use a novel method referred to as K2V that allows us to obtain the potential energy landscapes in terms of residue conformations extracted from molecular dynamics simulations at conformational equilibrium, and yields folding thermodynamic magnitudes in agreement with the experimental data available. <br>Our results demonstrate that the folded structures of the larger polyalanine chains are stabilized with respect to the folded structures of the shorter chains mostly by an increase of the entropic contribution of the solvent, which compensates the decrease of conformational entropy of the polypeptide, thus unveiling a key piece in the puzzle of protein folding.<br>In addition, the ability of the K2V method to provide the enthalpic and entropic contributions for individual residues along the peptide chain makes it clear that the entropic stabilization is basically governed by the nearest neighbor residues conformations, with the folding propensity being rationalized in terms of triads of residues.<br><br>

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