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1.
Nanda V Rosenblatt MM Osyczka A Kono H Getahun Z Dutton PL Saven JG Degrado WF 《Journal of the American Chemical Society》2005,127(16):5804-5805
Metal-binding sites in metalloproteins frequently occur at the interfaces of elements of secondary structure, which has enabled the retrostructural analysis of natural proteins and the de novo design of helical bundles that bind metal ion cofactors. However, the design of metalloproteins containing beta-structure is less well developed, despite the frequent occurrence of beta-conformations in natural metalloproteins. Here, we describe the design and construction of a beta-protein, RM1, that forms a stable, redox-active 4-Cys thiolate Fe(II/III) site analogous to the active site of rubredoxin. The protein folds into a beta-structure in the presence and absence of metal ions and binds Fe(II/III) to form a redox-active site that is stable to repeated cycles of oxidation and reduction, even in an aerobic environment. 相似文献
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Dotsevi Y. Sogah Daniele Perle-Treves N. Voyer W. F. Degrado 《Macromolecular Symposia》1994,88(1):149-163
A linear neutral repetitive peptide, (Leu-Gln-Pro)n (n = 1-100), an analog of the Ca2+ ion-binding domain of the matrix protein, amelogenin, has been synthesized. The polypeptide is mostly unordered in trifluoroethanol (TFE) at 25°C and its circular dichroism (CD) spectrum resembles that of the protein itself. In TFE the CD spectrum of (Leu-Gln-Pro)n reveals that the polypeptide interacts strongly with divalent cations Mg2+, Ca2+, Sr2+, and Ba2+ accompanied by conformational rearrangement from a random to a more-ordered one. In the presence of Li+, Na+ and K+ ions no such conformational change has been observed. The CD curves of the complexes suggest the presence of type I β-turns and reinforce the hypothesis that the region Gln112-Leu138 in amelogenin is the Ca2+-binding domain. In the solid state, powder X-ray diffraction suggests that the polymeric (LQP)n may exist as isolated “rigid rods”. 相似文献
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The first computationally designed self-assembling oligomer consisting of exclusively β-amino acids (βAAs) is presented. The packing of a β-3(14) helix into coiled-coils of varying stoichiometries as a function of amino acid sequence is examined. β-Peptides with hVal repeating every third residue in the sequence appeared to have a strong propensity to pack into hexameric bundles. The designed sequence was synthesized and characterized with CD spectroscopy, NMR, and analytical ultracentrifugation, suggesting that the peptide adopts a well-folded hexameric structure. 相似文献
4.
Lopez CF Nielsen SO Srinivas G Degrado WF Klein ML 《Journal of chemical theory and computation》2006,2(3):649-655
Knowledge of the mechanism of action of antimicrobial agents is crucial for the development of new compounds to combat microbial pathogens. To this end, computational studies on the interaction of known membrane-active antimicrobial polymers with phospholipid bilayers reveal spontaneous membrane insertion and cooperative action at low and high concentrations, respectively. In late-stage attack, antimicrobials cross the membrane core and occasionally align to provide a stepping-stone pathway for water permeation; this suggests a possible new mode of action that does not depend on pore formation for transport to and across the inner leaflet. The computations rationalize the observed activity of a new class of antimicrobial compounds. 相似文献
5.
Brown MK Degrado SJ Hoveyda AH 《Angewandte Chemie (International ed. in English)》2005,44(33):5306-5310
6.
Tatko CD Nanda V Lear JD Degrado WF 《Journal of the American Chemical Society》2006,128(13):4170-4171
Polar interactions have a profound influence on membrane stability and structure. A membrane-solubilized GCN4 peptide, MS-1, is used to study the impact of polar networks. Amide functionalities from amino acid side chains have been shown to promote peptide oligomerization, but lacked specificity. Herein, the hydrogen bonding interactions of an Asn side chain are coupled with the hydroxyl of Ser or Thr to generate a polar network. Analytical ultracentrifugation and fluorescence resonance energy transfer studies indicate that a trimer assembly is established where each membrane-embedded hydrogen bond contributes 1 kcal mol-1. 相似文献
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Korendovych IV Senes A Kim YH Lear JD Fry HC Therien MJ Blasie JK Walker FA Degrado WF 《Journal of the American Chemical Society》2010,132(44):15516-15518
The de novo design of membrane proteins remains difficult despite recent advances in understanding the factors that drive membrane protein folding and association. We have designed a membrane protein PRIME (PoRphyrins In MEmbrane) that positions two non-natural iron diphenylporphyrins (Fe(III)DPP's) sufficiently close to provide a multicentered pathway for transmembrane electron transfer. Computational methods previously used for the design of multiporphyrin water-soluble helical proteins were extended to this membrane target. Four helices were arranged in a D(2)-symmetrical bundle to bind two Fe(II/III) diphenylporphyrins in a bis-His geometry further stabilized by second-shell hydrogen bonds. UV-vis absorbance, CD spectroscopy, analytical ultracentrifugation, redox potentiometry, and EPR demonstrate that PRIME binds the cofactor with high affinity and specificity in the expected geometry. 相似文献
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The relationship between monomer chirality and polymer structure has been studied using both theoretical and experimental methods. Atomistic models, such as the ones employed in computational protein folding and design, can be used to study the relationship between monomer chirality and the properties of polypeptides. Using a simulated evolution approach that combines side-chain epimerization with backbone flexibility, we recapitulate the relationship between basic forces that drive secondary structure formation and sequence homochirality. Additionally, we find heterochiral motifs including a C-terminal helix capping interaction and stable helix-reversals that result in bent helix structures. Our studies show that simulated evolution of chirality with backbone flexibility can be a powerful tool in the design of novel heteropolymers with tuned stereochemical properties. 相似文献