The structure, energy, entropy, and dynamics of peptide crystals.
The structure, energy, entropy, and dynamics of peptide crystals.
复制标题
肽晶体的结构、能量、熵和动力学。
DOI：
10.1111/j.1749-6632.1986.tb20946.x
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发表时间：
1986
影响因子：
5.2
通讯作者：
Hagler,AT
中科院分区：
文献类型：
--
作者：
Kitson,DH;Avbelj,F;Eggleston,DS;Hagler,AT
Because of their fundamental role in living organisms, peptides and proteins have been an intensively studied class of molecules. Their function is intimately related to their structural and dynamic properties and a variety of experimental methods, including NMR spectroscopy1” and diffraction4 have been used to study these properties. Many important questions are, however, inaccessible to these experimental methods. For example, what forces drive a peptide to adopt the conformation that it takes up? Can we predict what this conformation will be, given only the sequence of amino acids in the peptide? Why does a peptide pack in the observed packing mode in a crystal? Hov-much strain is imposed on the molecule by the crystal lattice? In an attempt to answer such questions, a variety of theoretical methods have been used.’-’We have been applying several of these methods, including energy minimization and molecular dynamics, to study the structural, energetic, entropic, and dynamic properties of peptides in the crystal environment. In this paper we summarize extensive theoretical studies of three peptide crystal systems: N-formyl-Met-NMePhe-t-butyl ester, cyclo-(Ala-Pro-D-Phe),-8H, O and cyclo-(Gly-Pro-Gly),-4H20. We have carried out molecular dynamics simulations of these crystals, quenched, or minimized, the energy at points along the trajectory, calculated the entropy of the peptides in isolated and crystalline environments, and calculated their vibrational spectra. These studies were carried out with two overall objectives in mind. The first was to answer fundamental questions relating to peptide structure and dynamics and especially the effect of environment on these properties. The second was to take advantage of the excellent opportunity these systems provide to test the reliability of the theoretical methods that we employ. When energy minimization or molecular dynamics techniques are used for modeling peptide or protein systems, one obviously needs to have confidence that the results obtained accurately reflect the properties of the real system. This requirement can best be satisfied by attempting to calculate properties that are accessible experimentally, and peptide
