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Molecular modeling and dynamics of neuropeptide Y

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Summary

A combination of molecular modeling and molecular dynamics (MD) is used to determine a theoretical structure for neuropeptide Y (NPY). Starting with the X-ray structure for avian pancreatic polypeptide (APP), the substituted amino acids were mutated, the side chains oriented to local potential energy minima, and the entire structure minimized and subjected to an MD simulation. Comparison of the resulting NPY structure with APP X-ray and MD results showed secondary structural elements to be maintained and RMS fluctuations to be similar, although differences in both were observed. The approach presented offers a means to study the structure-function relationships of NPY and other similar polypeptides when combined with pharmacological measurements.

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Abbreviations

NPY:

Neuropeptide Y

APP:

Avian pancreatic polypeptide

ABNR:

Adopted-basis Newton Raphson

MD:

Molecular dynamics

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Author notes

  1. Alexander D. MacKerell Jr.

    Present address: Department of Chemistry, Harvard University, 12 Oxford Street, 02138, Cambridge, MA, USA

Authors and Affiliations

  1. Department of Medical Biophysics, Karolinska Institutet, 104 01, Stockholm, Sweden

    Alexander D. MacKerell Jr.

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  1. Alexander D. MacKerell Jr.
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MacKerell, A.D. Molecular modeling and dynamics of neuropeptide Y. J Computer-Aided Mol Des 2, 55–63 (1988). https://doi.org/10.1007/BF01532053

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  • DOI: https://doi.org/10.1007/BF01532053

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