Protein Science

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De novo design of the hydrophobic cores of proteins
Protein Science - Tập 4 Số 10 - Trang 2006-2018 - 1995
John R. Desjarlais, Tracy M. Handel
AbstractWe have developed and experimentally tested a novel computational approach for the de novo design of hydrophobic cores. A pair of computer programs has been written, the first of which creates a “custom” rotamer library for potential hydrophobic residues, based on the backbone structure of the protein of interest. The second program uses a genetic algorithm...... hiện toàn bộ
The structure of human pancreaticα-amylase at 1.8 Å resolution and comparisons with related enzymes
Protein Science - Tập 4 Số 9 - Trang 1730-1742 - 1995
Gary D. Brayer, Yaoguang Luo, Stephen G. Withers
Carbohydrate binding sites in a pancreatic α‐amylase‐substrate complex, derived from X‐ray structure analysis at 2.1 Å resolution
Protein Science - Tập 4 Số 4 - Trang 747-755 - 1995
Minxie Qian, Richard Haser, F. Payan
AbstractThe X‐ray structure analysis of a crystal of pig pancreatic α‐amylase (PPA, EC 3.2.1.1.) that was soaked with the substrate maltopentaose showed electron density corresponding to two independent carbohydrate recognition sites on the surface of the molecule. Both binding sites are distinct from the active site described in detail in our previous high‐resolut...... hiện toàn bộ
Estimation of the number of α‐helical and β‐strand segments in proteins using circular dichroism spectroscopy
Protein Science - Tập 8 Số 2 - Trang 370-380 - 1999
Narasimha Sreerama, S.Yu. Venyaminov, Robert W. Woody
AbstractA simple approach to estimate the number of α‐helical and β‐strand segments from protein circular dichroism spectra is described. The α‐helix and β‐sheet conformations in globular protein structures, assigned by DSSP and STRIDE algorithms, were divided into regular and distorted fractions by considering a certain number of terminal residues in a given α‐hel...... hiện toàn bộ
Outer membrane protein A of E. coli folds into detergent micelles, but not in the presence of monomeric detergent
Protein Science - Tập 8 Số 10 - Trang 2065-2071 - 1999
Jörg H. Kleinschmidt, Michael C. Wiener, Lukas K. Tamm
AbstractOuter membrane protein A (OmpA) of Escherichia coli is a β‐barrel membrane protein that unfolds in 8 M urea to a random coil. OmpA refolds upon urea dilution in the presence of certain detergents or lipids. To examine the minimal requirements for secondary and tertiary structure formation in β‐barrel membrane proteins, folding of ...... hiện toàn bộ
Motifs and structural fold of the cofactor binding site of human glutamate decarboxylase
Protein Science - Tập 7 Số 5 - Trang 1092-1105 - 1998
Kunbin Qu, David L. Martin, Charles E. Lawrence
AbstractThe pyridoxal‐P binding sites of the two isoforms of human glutamate decarboxylase (GAD65 and GAD67) were modeled by using PROBE (a recently developed algorithm for multiple sequence alignment and database searching) to align the primary sequence of GAD with pyridoxal‐P binding proteins of known structure. GAD's cofactor binding site is particularly interes...... hiện toàn bộ
The structure of a glycogen phosphorylase glucopyranose spirohydantoin complex at 1.8 Å resolution and 100 K: The role of the water structure and its contribution to binding
Protein Science - Tập 7 Số 4 - Trang 915-927 - 1998
Mary Gregoriou, M.E.M. Noble, Kimberly A. Watson, Elspeth F. Garman, Thomas M. Krülle, C. de la Fuente, M. Carmen de la Fuente, N G Oikonomakos, L.N. Johnson
AbstractA glucopyranose spirohydantoin (a pyranose analogue of the potent herbicide, hydantocidin) has been identified as the highest affinity glucose analogue inhibitor of glycogen phosphorylase b (GPb). In order to elucidate the structural features that contribute to the binding, the structures of GPb in the native T state conformation and in complex with glucopy...... hiện toàn bộ
Protein structure refinement based on paramagnetic NMR shifts: Applications to wild‐type and mutant forms of cytochrome c
Protein Science - Tập 4 Số 2 - Trang 296-305 - 1995
Miriam Gochin, Heinrich Röder
AbstractA new approach to NMR solution structure refinement is introduced that uses paramagnetic effects on nuclear chemical shifts as constraints in energy minimization or molecular dynamics calculations. Chemical shift differences between oxidized and reduced forms of horse cytochrome c for more than 300 protons were used as constraints...... hiện toàn bộ
The 1.9 Å crystal structure of Escherichia coli MurG, a membrane‐associated glycosyltransferase involved in peptidoglycan biosynthesis
Protein Science - Tập 9 Số 6 - Trang 1045-1052 - 2000
Sha Ha, David Walker, Yigong Shi, Suzanne Walker
AbstractThe 1.9 Å X‐ray structure of a membrane‐associated glycosyltransferase involved in peptidoglycan biosynthesis is reported. This enzyme, MurG, contains two α/β open sheet domains separated by a deep cleft. Structural analysis suggests that the C‐terminal domain contains the UDP‐GlcNAc binding site while the N‐terminal domain contains the acceptor binding sit...... hiện toàn bộ
Unassisted refolding of urea‐denatured arginine kinase from shrimp Feneropenaeus chinensis: Evidence for two equilibrium intermediates in the refolding pathway
Protein Science - Tập 13 Số 7 - Trang 1892-1901 - 2004
Ji-Cheng Pan, Zhenhang Yu, Xiaoyang Su, Yingxin Sun, Xue-Ming Rao, Hai‐Meng Zhou
AbstractThe refolding process and the equilibrium intermediates of urea‐denatured arginine kinase (AK) were investigated by 1‐anilino‐8‐naphthalenesulfonate (ANS) intrinsic fluorescence, far‐UV circular dichroism (CD), size‐exclusion chromatography (SEC), and enzymatic activity. In dilute denaturant, two equilibrium refolding intermediates (I and N′) were discovere...... hiện toàn bộ
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