RESEARCH ARTICLE

 

Computer simulation studies of trishomocubane heptapeptide of the type Ac-Ala₃-Tris-Ala₃-NHMe

 

 

Parvesh Singh^I; Krishna Bisetty^{I, *}; Penny Govender^II; Gert Kruger^III

^IDepartment of Chemistry, Durban University of Technology, Steve Biko campus, P. O. Box 1334, Durban, 4000 South Africa
^IIDepartment of Chemistry, University of Johannesburg, South Africa
^IIISchool of Chemistry, University of KwaZulu-Natal, Durban, 4041 South Africa

 

 

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ABSTRACT

As part of an extension on the cage peptide chemistry, the present work involves an assessment of the conformational profile of trishomocubane heptapeptide of the type Ac-Ala₃-Tris-Ala₃-NHMe using molecular dynamics (MD) simulations. All MD protocols were explored within the framework of a molecular mechanics approach using the PARM94 force field parameters modified in-house to mimic the implicit and explicit solvent conditions. The 50 ns MD trajectories revealed a tendency of the trishomocubane polypeptide to adopt bent conformations in vacuo, MEOH and TIP3P solvent models, consistent with previous studies undertaken in our laboratory. The aim of this paper is to exemplify the tendency of the highly constrained cage residues to promote reverse-turn characteristics in the polypeptide chains, which could play a pivotal role in the design of new cage peptidomimetics.

Keywords: Trishomocubane, molecular dynamics, Amber, CLASICO, β-turn, α-helical

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Full text available only in pdf format.

 

Acknowledgements

PS gratefully acknowledges financial support from the Durban University of Technology and the National Research Foundation for the position of a Research Associate. KB gratefully acknowledges the experiences and insights gained from the Spanish collaborators (Professor Juan J. Perez and co-workers) through the SA-Spain bilateral agreement.

 

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Received 1 March 2011
Revised 4 April 2011
Accepted 25 May 2011

 

 

Submitted by invitation to celebrate 2011 the 'International Year of Chemistry'.
* To whom correspondence should be addressed. E-mail: bisettyk@dut.ac.za