Quantum Chemical Calculations on Small Protein Models

Jákli, Imre; Perczel, András; Viskolcz, Béla; Csizmadia, Imre G.

doi:10.1007/978-3-319-09976-7_2

Cited by 3 publications

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References 139 publications

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“…The side chains (R) of the 20 different amino acids contain 1-18 atoms 23 . The flexibility may also involve several dihedral angles of the side chain variation up five dimensions (5D) 24 . The backbone, in Figure 10, has two dihedral angles and each of this is a 3-fold rotational potential, consequently, it is expected to exhibit 3 2 =9 conformers.…”

Section: Figure 9 the Twenty Different Amino Acidsmentioning

confidence: 99%

Analytical functional representation of quantum chemical potential energy curves and surfaces

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Section: Figure 9 the Twenty Different Amino Acidsmentioning

confidence: 99%

Analytical functional representation of quantum chemical potential energy curves and surfaces

Rágyanszki¹

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An improved two-rotor function for conformational potential energy surfaces of 20 amino acid diamides

et al. 2018

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Predicting the three-dimensional structure of a protein from its amino acid sequence requires a complete understanding of the molecular forces that influences the protein folding process. Each possible conformation has its corresponding potential energy, which characterizes its thermodynamic stability. This is needed to identify the primary intra- and inter-molecular interactions, so that we can reduce the dimensionality of the problem, and create a relatively simple representation of the system. Investigating this problem using quantum chemical methods produces accurate results; however, this also entails large computational resources. In this study, an improved two-rotor potential energy function is proposed to represent the backbone interactions in amino acids through a linear combination of a Fourier series and a mixture of Gaussian functions. This function is applied to approximate the 20 amino acid diamide Ramachandran-type PESs, and results yielded an average RMSE of 2.36 kJ mol−1, which suggest that the mathematical model precisely captures the general topology of the conformational potential energy surface. Furthermore, this paper provides insights on the conformational preferences of amino acid diamides through local minima geometries and energy ranges, using the improved mathematical model. The proposed mathematical model presents a simpler representation that attempts to provide a framework on building polypeptide models from individual amino acid functions, and consequently, a novel method for rapid but accurate evaluation of potential energies for biomolecular simulations.

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A prelude to building mathematical models for polypeptide folding: analysis on the conformational potential energy hypersurface cross-sections of N-acetyl-glycyl-glycine-N′-methylamide

et al. 2018

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Finding a relationship on how a three-dimensional protein folds from its linear amino acid chain gets more complex with increasing chain length, so working on a smaller peptide conformational problem can provide initial ideas on what are the main molecular forces and how these influence the folding process. Following the study of conformations of amino acid units entering the proteins to understand the secondary structure of small peptides, this paper proposes mathematical models for the several two-rotor cross-sections of the five-dimensional N-acetyl-glycyl-glycine-N′-methylamide potential energy hypersurface (PEHS). These cross-sections are extracted along the first glycine subunit, with its coordinates fixed at the five energy minima of the glycine diamide. The resulting mathematical models yield an average RMSE of 1.36 kJ mol−1 and an average R2 of 0.9923 with respect to energy values obtained from DFT calculations. The minima geometries obtained from these models are also in good agreement with DFT-optimized energy minima conformers. An important aspect of this study also tackles the relationship between the PEHS of the glycyl-glycine diamide and its glycine subunits. It has been observed that there are deviations up to 28.35 kJ mol−1 and 29.52 kJ mol−1 between the PEHS cross-sections along γL and γD conformations, respectively, in the first glycine subunit. This may suggest that there are significant backbone–backbone intermolecular forces acting on the dipeptide. The abovementioned findings can help in developing more complex mathematical models for polypeptide folding from amino acid subunits.

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Quantum Chemical Calculations on Small Protein Models

Cited by 3 publications

References 139 publications

Analytical functional representation of quantum chemical potential energy curves and surfaces

Analytical functional representation of quantum chemical potential energy curves and surfaces

An improved two-rotor function for conformational potential energy surfaces of 20 amino acid diamides

A prelude to building mathematical models for polypeptide folding: analysis on the conformational potential energy hypersurface cross-sections of N-acetyl-glycyl-glycine-N′-methylamide

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