Computational Study of a Heterostructural Model of Type I Collagen and Implementation of an Amino Acid Potential Method Applicable to Large Proteins
| Autor: | Paul Rulis, Jay Eifler, Rex Tai, Wai-Yim Ching |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2014 |
| Předmět: |
H-bonding
collagen model density functional theory (DFT) calculations electronic structure amino-acids large proteins Polymers and Plastics Hydrogen bond Chemistry Ab initio Potential method General Chemistry Electronic structure Bond order lcsh:QD241-441 lcsh:Organic chemistry Chemical physics Computational chemistry Density of states Density functional theory Type I collagen |
| Zdroj: | Polymers; Volume 6; Issue 2; Pages: 491-514 Polymers, Vol 6, Iss 2, Pp 491-514 (2014) |
| ISSN: | 2073-4360 |
| DOI: | 10.3390/polym6020491 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|