Trialanine (Ala-Ala-Ala) may be used along with other short chain alanines, tetra- and penta-alanine, as model compounds to study physicochemical parameters of small peptides.
Physical chemistry chemical physics : PCCP, 11(40), 9149-9159 (2009-10-09)
A molecular mechanics (MM) force field-based empirical electrostatic potential map (MM map) for amide-I vibrations is developed with the aim of seeking a quick and reasonable approach to computing local mode parameters and their distributions in solution phase. Using N-methylacetamide
The Journal of chemical physics, 138(7), 074111-074111 (2013-03-01)
An open-shell extension of the pair interaction energy decomposition analysis (PIEDA) within the framework of the fragment molecular orbital (FMO) method is developed. The open-shell PIEDA method allows the analysis of inter- and intramolecular interactions in terms of electrostatic, exchange-repulsion
Thrombosis and haemostasis, 113(2), 290-304 (2014-11-22)
The integrin αIIbβ3 on resting platelets can bind to immobilised fibrinogen resulting in platelet spreading and activation but requires activation to bind to soluble fibrinogen. αIIbβ3 is known to interact with the general integrin-recognition motif RGD (arginine-glycine-aspartate) as well as
The journal of physical chemistry. B, 113(9), 2922-2932 (2009-02-27)
The conformational preference of individual amino acid residues in the unfolded state of peptides and proteins is the subject of a continuous debate. Research has mostly been focused on alanine, owing to its abundance in proteins and its relevance for
The Journal of chemical physics, 130(21), 214108-214108 (2009-06-11)
Biomolecular systems are inherently hierarchic and many simulation methods that try to integrate atomistic and coarse-grained (CG) models have been proposed, which are called multiscale simulations. Here, we propose a new multiscale molecular dynamics simulation method which can achieve high
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