Theory of Phase Transitions in Polypeptides and Proteins

Yakubovich, Alexander V.

doi:10.1007/978-3-642-22592-5

Cited by 2 publications

(2 citation statements)

References 110 publications

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“…Amino acids are organic compounds that are consisted of Amino (COOH) (-COOH) which is basic and Carboxyl (COOH) (-COOH) which is possessed an acidic character. They have directly affected gene expression and control of the function of proteins [1].Proteins are linear polymers that fold into specific and ordered three-dimensional conformations based on their amino acid sequences [2], [3]. Their folding is a vital parameter that determines protein effectiveness in biological processes and this folding process is driven by thermodynamic stability.…”

Section: Introductionmentioning

confidence: 99%

Investigation of Solid Formation Enthalpy and Molecular Mechanics Energies of Amino Acids via Force Field Approach

SONGUR>¹,

ORHAN>

Özgen

2023

Bitlis Eren Üniversitesi Fen Bilimleri Dergisi

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Accurate determination of the thermodynamic and molecular mechanical properties of amino acids will contribute to a better understanding of their folding mechanisms. In this study, the enthalpy values and molecular mechanics parameters of 17 amino acids were investigated by the classical molecular dynamics method. All calculations were performed using the force-field potential approach. As a result, the calculated solid formation enthalpy for ALA, ASN, ASP, CYS, LYS, and PHE are in good agreement with the experimental data. In addition, molecular mechanics parameters such as Coulomb, bond, angle, dihedral, and Van der Waals were calculated for all amino acids. It is seen that the Coulomb energy is quite low compared to the rest of the molecular mechanical energies. The molecular mechanical energies obtained from the study will contribute to protein-lipid modification studies for electronic interaction, ligand binding to the cell surface, and correct protein localization.

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Section: Introductionmentioning

confidence: 99%

Investigation of Solid Formation Enthalpy and Molecular Mechanics Energies of Amino Acids via Force Field Approach

SONGUR>¹,

ORHAN>

Özgen

2023

Bitlis Eren Üniversitesi Fen Bilimleri Dergisi

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“…The problem of protein folding is conceptually related to the studies of conformational transitions in short polypeptide chains [4,5,[22][23][24], and the dynamics of polypeptide chains can be described computationally at the relevant spatial and temporal scales. Several earlier studies employed ab initio and classical mechanics methods to investigate properties and dynamics of polypeptides in vacuum [22,[24][25][26][27][28]. It was shown that the backbone dihedral angles φ and ψ (see Fig.…”

Section: Introductionmentioning

confidence: 99%

Studying folding $$\leftrightarrow $$ unfolding dynamics of solvated alanine polypeptides using molecular dynamics

et al. 2022

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The atomistic description of the folding process of a structureless chain of amino acids to a functioning protein is still considered to be a challenge for computational biophysics. An in-depth understanding of protein-folding can be achieved through atomistic dynamics accounting for the solvent effects, combined with the theoretical description of conformational changes in shorter polypeptide chains. The present paper studies the folding transitions in short polypeptide chains consisting of 11 alanine residues in explicit solvent employing all-atom molecular dynamics. The multiple observed folding $$\leftrightarrow $$ ↔ unfolding events of the peptide are interpreted as a dynamic process and rationalised through the analysis of the potential energy surface of the system. It is demonstrated that alanine polypeptide folding dynamics is governed by the backbone dihedral angles and involves the formation of spontaneously folded $$\alpha $$ α -helices which emerge and live for ca. 1–20 picoseconds. The helical content within the polypeptide at different temperatures was quantified through a statistical mechanics approach, which showed a reasonable agreement with the results of molecular dynamics simulations and experiments performed for alanine-rich peptides. Graphical abstract

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Theory of Phase Transitions in Polypeptides and Proteins

Cited by 2 publications

References 110 publications

Investigation of Solid Formation Enthalpy and Molecular Mechanics Energies of Amino Acids via Force Field Approach

Investigation of Solid Formation Enthalpy and Molecular Mechanics Energies of Amino Acids via Force Field Approach

Studying folding $$\leftrightarrow $$ unfolding dynamics of solvated alanine polypeptides using molecular dynamics

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