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

1
Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA
2
Weinberg School of Arts and Sciences, Northwestern University, Evanston, IL 60201, USA
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Author to whom correspondence should be addressed.
Polymers 2014, 6(2), 491-514; https://doi.org/10.3390/polym6020491
Received: 7 January 2014 / Revised: 8 February 2014 / Accepted: 11 February 2014 / Published: 18 February 2014
(This article belongs to the Special Issue Computational Chemistry)
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. View Full-Text
Keywords: collagen model; density functional theory (DFT) calculations; electronic structure; H-bonding; amino-acids; large proteins collagen model; density functional theory (DFT) calculations; electronic structure; H-bonding; amino-acids; large proteins
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Eifler, J.; Rulis, P.; Tai, R.; Ching, W.-Y. Computational Study of a Heterostructural Model of Type I Collagen and Implementation of an Amino Acid Potential Method Applicable to Large Proteins. Polymers 2014, 6, 491-514.

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