Paper Citing NAMD - Abstract
Siggel, L.; Molnar, F.
Computer modelling of a type-1 collagen fibril in water. 1. Model development and validation
JOURNAL OF THE AMERICAN LEATHER CHEMISTS ASSOCIATION, 101:179-+, MAY 2006
Type-1 collagen is the principle component of hides used to produce leather. The amino acid sequence for calf skin type-1 collagen is known, as well as the macroscopic structure as seen in electron micrographs. However, little is known about the intermediate scale or atomistic level. With our Work we have established a state-of-the-art molecular model of a collagen fibril that is large enough to mimic parts of the fibrilar system and provide molecular level detail about the changes in structure and properties due to varying pH or the effect of leather chemicals and dyes. This paper covers the construction and validation of the varying models which evolved in the Course of the work. The density and swelling behavior as a function of pH, as well as "pickling" with 12% NaCl was qualitatively reproduced. In both experiment and Our simulation, swelling occurs at very high and low pH. but not in the neutral system or the acidic system when 12% NaCl is first added ("pickling"). The mobility of water in the systems of varying pH was studied and show that water is surprisingly mobile in the fibril when compared to diffusion in the bulk. The interaction of side chains in collagen with one another at the differing pH's encountered during tanning was also examined.
