Picture of person typing on laptop with programming code visible on the laptop screen

World class computing and information science research at Strathclyde...

The Strathprints institutional repository is a digital archive of University of Strathclyde's Open Access research outputs. Strathprints provides access to thousands of Open Access research papers by University of Strathclyde researchers, including by researchers from the Department of Computer & Information Sciences involved in mathematically structured programming, similarity and metric search, computer security, software systems, combinatronics and digital health.

The Department also includes the iSchool Research Group, which performs leading research into socio-technical phenomena and topics such as information retrieval and information seeking behaviour.


Solvent effects and hydration of a tripeptide in sodium halide aqueous solutions: an in silico study

Fedorov, Maxim V. and Goodman, Jonathan M. and Schumm, Stephan (2007) Solvent effects and hydration of a tripeptide in sodium halide aqueous solutions: an in silico study. Physical Chemistry Chemical Physics, 9 (40). pp. 5423-5435. ISSN 1463-9076

Full text not available in this repository. Request a copy from the Strathclyde author


In this work we are trying to gain insight into the mechanisms of ion-protein interactions in aqueous media at the molecular scale through fully atomistic molecular dynamics simulations. We present a systematic molecular simulation study of interactions of sodium and halide ions with a trialanine peptide in aqueous sodium halide solutions with different salts concentrations ( 0.20, 0.50, 1.0 and 2.0 M). Each simulation covers more than fifty nanoseconds to ensure the convergence of the results and to enable a proper determination of the tripeptide-ion interactions through the potentials of mean force. Changes in ion densities in the vicinity of different peptide groups are analysed and implications for the tripeptide conformations are discussed.