Conformational Energy Studies of Model Silk Fibroin Peptides
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CONFORMATIONAL ENERGY STUDIES OF MODEL SILK FIBROIN PEPTIDES STEPHEN A. FOSSEY*, G. Nemethy, K. D. Gibson, and H. A. Scheraga, Baker Laboratory of Chemistry, Cornell University, Ithaca, New York 14853-1301. *On leave from US Army Natick Research, Development and Engineering Center, Natick, Massachusetts 01760-5020 Silk-like proteins are a topic of long-standing scientific interest and recently are being considered for such uses as high performance fibers [1] and enzyme-immobilizing substrates [2]. The structure of silk (in particular, the metastable silk I form) is critical in understanding the formation and processing of these materials. Computations provide a useful tool for the detailed modeling of the structures of fibrous proteins. Conformational energy calculations on representative model polypeptides have been used successfully to elucidate the structure of collagen [3]. We have applied this method to the study of the crystalline region of Bombvx mori silk fibroin [4]. The crystalline domains of B. mori silk fibroin exist in one of two morphologies. The more stable form is composed of stacked beta sheets [5) known as silk II. The less stable form, known as silk I or water-soluble silk, has remained poorly understood. Attempts to induce orientation of the polymer chains for experimental analysis tend to cause the silk I form to convert to the more stable silk II conformation. We have used the model sequence CH 3 CO-Ala-Gly-Ala-Gly-Ala-Gly-NHCH 3 to represent the crystalline regions. Strands of this sequence have been used to construct hydrogen-bonded sheets. These sheets have then been stacked to model three-dimensional crystals. The calculations were carried out by using the ECEPP/2 (Empirical Conformational Energy Program for Peptides) algorithm on the IBM 3090-600E supercomputer at the Cornell National Supercomputer Facility. First, the conformational energy of isolated sheets of five strands of both parallel and antiparallel chains were minimized. The starting dihedral angles for all residues of a given sheet were chosen to lie along the diagonal of a (• ,$&) plot at 10 degree intervals from -0V1- 80 to 180 degrees. These calculations include a new analytical expression for the first derivative of the potential energy function with respect to the rigid body variables of the individual chains. For both parallel and antiparallel sheets, two chain arrangements were minimized, viz. sheets in which all alanine side chains projected from the same side of the sheet (referred to as in-register) and sheets in which the alanine side chains projected from both sides of the sheet referred to as out-of-register) (see figure 1). For every one of these four arrangements, one conformational energy minimum was found in the E region and one in the C region of the (0 , ) map. Some minimizations of antiparallel out-of-register sheets resulted in a third minimum, viz. a sheet where the alanine residues adopted dihedral angles of (0 ,* ) -(-800,1500) and the glycine sheet residues adopted diheral angles of (0 , ) -(-150 ,800)
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