Computational Study of a Heterostructural Model of Type I Collagen and Implementation of an Amino Acid Potential Method Applicable to Large Proteins

Abstract

Collagen molecules are the primary structural proteins of many biological systems. Much progress has been made in the study of the structure and function of collagen, but fundamental understanding of its electronic structures at the atomic level is still lacking. We present the results of electronic structure and bonding calculations of a specific model of type I collagen using the density functional theory-based method. Information on density of states (DOS), partial DOS, effective charges, bond order values, and intra-and inter-molecular H-bonding are obtained and discussed. We further devised an amino-acid-based potential method (AAPM) to circumvent the full self-consistent field (SCF) calculation that can be applied to large proteins. The AAPM is validated by comparing the results with the full SCF calculation of the whole type I collagen model with three strands. The calculated effective charges on each atom in the model retained at least 95% accuracy. This technique provides a viable and efficient way to study the electronic structure of large complex biomaterials at the ab initio level.

Electronic Structure and Partial Charge Distribution of Doxorubicin in Different Molecular Environments

“…This method is particularly efficient for calculating the electronic structure of large complex systems, especially in the case of biomolecules 29. The OLCAO method has been employed in the study of many other complex systems, such as inorganics,30 organics,31 supercooled water,32 and biomaterials,33, 34 in the last decade. In the present calculation, a full basis, which consisted of the core orbitals, occupied valence orbitals, and the next empty shell of unoccupied orbitals for each atom, was used for the determination of the self‐consistent potential and calculations of the density of states (DOS).…”

Ab initio Modeling of the Electronic Structures and Physical Properties of a‐Si1−xGexO2 Glass (x = 0 to 1)

“…VASP is used for structural relaxation and calculation of mechanical and elastic properties and OLCAO is used to calculate the electronic structures, bonding, and optical properties. The OLCAO method is specially designed to study the electronic and spectroscopic properties of complex crystals, amorphous solids, 34,35 liquids, and biomolecular systems 36,37 because of its efficiency in using the localized atomic orbitals for the basis expansion and special technique in evaluating multicenter integrals using Gaussian transformation. 33 It is most effective when the complex structure is first optimized by plane wave-based method such as VASP and then followed by OLCAO method for properties evaluation.…”

Charge distribution and hydrogen bonding of a collagen α2‐chain in vacuum, hydrated, neutral, and charged structural models

“…There are many studies on different structure models for collagen . The three models based on the α 2 ‐chain of collagen used in the present work has the same origin as used in our earlier study . We stress that this model is used solely for the investigation of a typical protein under different environments, not for any specific properties of collagen per se.…”

“…Here, we report on a detailed computational study on the α 2 ‐chain model of collagen as a representative peptide to study the effect of solvation and protonation/deprotonation on some of its side chains. This α 2 ‐chain model is similar to the one in a previous study, which has a triplet of two α 1 ‐chains and one α 2 ‐chain in the development of a computational scheme, the so‐called Amino Acid Potential Method (AAPM) . In this work, we start with this model to examine collagen α 2 ‐chain as a representative protein of reasonable size in three different environments and modifications, namely in vacuum, the solvated form with water molecules, and a model with modifications of certain charged sites due to addition or removal of a proton at the site.…”