Exploration of the Four-Dimensional-Conformational Potential Energy Hypersurface of N-Acetyl-l-aspartic Acid N‘-Methylamide with Its Internally Hydrogen Bonded Side-Chain Orientation

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

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.

Comprehensive analysis of energy minima of the 20 natural amino acids

Energy minima of the 20 natural amino acids (capped by a peptide bond at both the N and the C termini, CH3-C(═O)-N(H)-(H)Cα(R)-C(═O)-N(H)-CH3), were obtained by ab initio geometry optimization. Starting with a large number of minima, quickly generated by MarvinView, geometry optimization at the HF/6-31G(d,p) level of theory reduced the number of minima, followed by further optimization at the B3LYP/apc-1 and MP2/cc-pVDZ levels, which caused some minima to disappear and some stable minima to migrate on the Ramachandran map. There is a relation between the number of minima and the size and the flexibility of the side chain. The energy minima of the 20 amino acids are mainly located in the regions of βL, γL, δL, and αL of the Ramachandran map. Multipole moments of atoms occurring in the fragment [-NH-Cα-C(═O)-] common to all 20 amino acids were calculated at the three levels of theory mentioned above. The near parallelism in behavior of these moments between levels of theory is beneficial toward estimating moments with the more expensive B3LYP and MP2 methods from data calculated with the cheaper HF method. Finally, we explored the transferability of properties between different amino acids: the bond length and angles of the common fragment [-NH-Cα(HαCβ)-C'(═O)-] in all amino acids except Gly and Pro. All bond lengths are highly transferable between different amino acids, and the standard deviations are small.

Quantum chemical investigations on intraresidue carbonyl-carbonyl contacts in aspartates of high-resolution protein structures

The folding and stability of a polypeptide chain are due to many different and simultaneous noncovalent interactions. Recent studies have observed several novel and counterintuitive contacts in protein structures, and the nature of interactions due to such contacts is yet to be fully elucidated. We have identified carbonyl-carbonyl intraresidue contacts in 102 Asp residues from a data set of high-resolution protein structures. At the outset, it appears that such close approach of two carbonyl oxygen atoms is energetically not favorable. We have carried out ab initio quantum chemical calculations on 10 representative examples of self-contacting Asp residues from different regions of the Ramachandran map. Potential energy scan using three levels of theory (HF, B3LYP, and MP2) and two basis sets (6-31+G* and 6-31++G**) was performed by varying the side-chain dihedral angle chi(1) while keeping all other parameters corresponding to that observed in the protein structures. We also calculated interaction energies by considering the surrounding interacting residues and water molecules. Our results show that the energy difference between a self-contacting Asp residue from the crystal structures and the minimum energy conformations is about 10-15 kcal/mol. This small energy difference is compensated by its interactions with the surrounding residues and water molecules as observed in the interaction energy analysis. The results are independent of the levels of theory used. The contacting carbonyl-carbonyl groups adopt a sheared parallel motif orientation which helps to expose both the backbone and side-chain carbonyl oxygen atoms and enable them to participate in tertiary interactions. Natural bond orbital calculations indicate that carbonyl-carbonyl groups in self-contacting Asp residues interact through n --> pi* electron delocalization. The geometry analysis and nature of chemical interactions together explain the rationale for the existence of such Asp residues in protein structures and their importance in the protein stability.

Resonant infrared multiphoton dissociation spectroscopy of gas-phase protonated peptides. Experiments and Car–Parrinello dynamics at 300 K

The gas-phase structures of protonated peptides are studied by means of resonant infrared multiphoton dissociation spectroscopy (R-IRMPD) performed with a free electron laser. The peptide structures and protonation sites are obtained through comparison between experimental IR spectra and their prediction from quantum chemistry calculations. Two different analyses are conducted. It is first supposed that only well-defined conformations, sufficiently populated according to a Boltzmann distribution, contribute to the observed spectra. On the contrary, DFT-based Car-Parrinello molecular dynamics simulations show that at 300 K protonated peptides no longer possess well-defined structures, but rather dynamically explore the set of conformations considered in the first conventional approach.