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Structural Basis for Exquisite Specificity of Affinity Clamps, Synthetic Binding Proteins Generated through Directed Domain-interface Evolution
[作者：Huang, J; Makabe, K; Biancalana, M; Koide, A; Koide, S,期刊：Journal of Molecular Biology, 页码：1221-1231 , 文章类型： Article，,卷期：2009年392-5]
We have established a new protein-engineering strategy termed "directed domain-interface evolution" that generates a binding site by linking two protein domains and then optimizing the interface between them. Using this ...

Catalytic Mechanism of Retaining alpha-Galactosidase Belonging to Glycoside Hydrolase Family 97
[作者：Okuyama, M; Kitamura, M; Hondoh, H; Kang, MS; Mori, H; Kimura, A; Tanaka, I; Yao, M,期刊：Journal of Molecular Biology, 页码：1232-1241 , 文章类型： Article，,卷期：2009年392-5]
Glycoside hydrolase family 97 (GH 97) is a unique glycoside family that contains inverting and retaining glycosidases. Of these, BtGH97a (SusB) and BtGH97b (UniProtKB/TrEMBL entry QM6L0), derived from Bacteroides thetaio...

Crystal Structures of alpha-Crystallin Domain Dimers of alpha B-Crystallin and Hsp20
[作者：Bagneris, C; Bateman, OA; Naylor, CE; Cronin, N; Boelens, WC; Keep, NH; Slingsby, C,期刊：Journal of Molecular Biology, 页码：1242-1252 , 文章类型： Article，,卷期：2009年392-5]
Small heat shock proteins (sHsps) are a family of large and dynamic oligomers highly expressed in long-lived cells of muscle, lens and brain. Several family members are upregulated during stress, and some are strongly...

Interaction between Intrinsically Disordered Proteins Frequently Occurs in a Human Protein-Protein Interaction Network
[作者：Shimizu, K; Toh, H,期刊：Journal of Molecular Biology, 页码：1253-1265 , 文章类型： Article，,卷期：2009年392-5]
Intrinsic protein disorder is a widespread phenomenon characterised by a lack of stable three-dimensional structures and is considered to play an important role in protein-protein interactions (PPIs). This study examined...

Structural Basis of Substrate Specificity of Plant 12-Oxophytodienoate Reductases
[作者：Breithaupt, C; Kurzbauer, R; Schaller, F; Stintzi, A; Schaller, A; Huber, R; Macheroux, P; Clausen, T,期刊：Journal of Molecular Biology, 页码：1266-1277 , 文章类型： Article，,卷期：2009年392-5]
12-Oxophytodienoate reductase 3 (OPR3) is a FMN-dependent oxidoreductase that catalyzes the reduction of the cyclopentenone (9S,13S)-12-oxophytodienoate [(9S,13S)-OPDA] to the corresponding cyclopentanone in the biosynth...

Positively Cooperative Binding of Zinc Ions to Bacillus cereus 569/H/9 beta-Lactamase II Suggests that the Binuclear Enzyme Is the Only Relevant Form for Catalysis
[作者：Jacquin, O; Balbeur, D; Damblon, C; Marchot, P; De Pauw, E; Roberts, GCK; Frere, JM; Matagne, A,期刊：Journal of Molecular Biology, 页码：1278-1291 , 文章类型： Article，,卷期：2009年392-5]
Metallo-beta-lactamases catalyze the hydrolysis of most beta-lactam antibiotics and hence represent a major clinical concern. While enzymes belonging to subclass B1 have been shown to display maximum activity as dizinc s...

Crystal Structures of Glycosyltransferase UGT78G1 Reveal the Molecular Basis for Glycosylation and Deglycosylation of (Iso)flavonoids
[作者：Modolo, LV; Li, LN; Pan, HY; Blount, JW; Dixon, RA; Wang, XQ,期刊：Journal of Molecular Biology, 页码：1292-1302 , 文章类型： Article，,卷期：2009年392-5]
The glycosyltransferase UGT78G1 from Medicago truncatula catalyzes the glycosylation of various (iso)flavonoids such as the flavonols kaempferol and myricetin, the isoflavone formononetin, and the anthocyanidins pelar...

The Limited Role of Nonnative Contacts in the Folding Pathways of a Lattice Protein
[作者：Gin, BC; Garrahan, JP; Geissler, PL,期刊：Journal of Molecular Biology, 页码：1303-1314 , 文章类型： Article，,卷期：2009年392-5]
Models of protein energetics that neglect interactions between amino acids that are not adjacent in the native state, such as the Go model, encode or underlie many influential ideas on protein folding. Implicit in this s...

Thermodynamics of Loop Formation in the Denatured State of Rhodopseudomonas palustris Cytochrome c ': Scaling Exponents and the Reconciliation Problem
[作者：Rao, KS; Tzul, FO; Christian, AK; Gordon, TN; Bowler, BE,期刊：Journal of Molecular Biology, 页码：1315-1325 , 文章类型： Article，,卷期：2009年392-5]
The observation that denatured proteins yield scaling exponents, nu, consistent with random-coil behavior and yet can also have pockets of residual or nonrandom structure has been termed the "reconciliation problem". To ...

The Folding Pathway of the Antibody V-L Domain
[作者：Simpson, ER; Herold, EM; Buchner, J,期刊：Journal of Molecular Biology, 页码：1326-1338 , 文章类型： Article，,卷期：2009年392-5]
Antibodies are modular proteins consisting of domains that exhibit a beta-sandwich structure, the so-called immunoglobulin fold. Despite structural similarity, differences in folding and stability exist between differ...

Pathways and Mechanisms for Product Release in the Engineered Haloalkane Dehalogenases Explored Using Classical and Random Acceleration Molecular Dynamics Simulations
[作者：Klvana, M; Pavlova, M; Koudelakova, T; Chaloupkova, R; Dvorak, P; Prokop, Z; Stsiapanava, A; Kuty, M; Kuta-Smatanova, I; Dohnalek, J; Kulhanek, P; Wade, RC; Damborsky, J,期刊：Journal of Molecular Biology, 页码：1339-1356 , 文章类型： Article，,卷期：2009年392-5]
Eight mutants of the DhaA haloalkane dehalogenase carrying mutations at the residues lining two tunnels, previously observed by protein X-ray crystallography, were constructed and biochemically characterized. The mutants...

The Structure and Conformation of Lys63-Linked Tetraubiquitin
[作者：Datta, AB; Hura, GL; Wolberger, C,期刊：Journal of Molecular Biology, 页码：1117-1124 , 文章类型： Article，,卷期：2009年392-5]
Ubiquitination involves the covalent attachment of the ubiquitin (Ub) C-terminus to the lysine side chain of a substrate protein by an isopeptide bond. The modification can comprise a single Ub moiety or a chain of Ub mo...

Crystal Structure of the GluR2 Amino-Terminal Domain Provides Insights into the Architecture and Assembly of Ionotropic Glutamate Receptors
[作者：Clayton, A; Siebold, C; Gilbert, RJC; Sutton, GC; Harlos, K; McIlhinney, RAJ; Jones, EY; Aricescu, AR,期刊：Journal of Molecular Biology, 页码：1125-1132 , 文章类型： Article，,卷期：2009年392-5]
Ionotropic glutamate receptors are functionally diverse but have a common architecture, including the 400-residue amino-terminal domain (ATD). We report a 1.8-angstrom resolution crystal structure of human GluR2-ATD. ...

One Is Not Enough
[作者：Daber, R; Sharp, K; Lewis, M,期刊：Journal of Molecular Biology, 页码：1133-1144 , 文章类型： Article，,卷期：2009年392-5]
In both prokaryotic and eukaryotic organisms, repressors and activators are responsible for regulating gene expression. The lac operon is a paradigm for understanding how metabolites function as signaling molecules and m...

Acceleration of 5-Methylcytosine Deamination in Cyclobutane Dimers by G and Its Implications for UV-Induced C-to-T Mutation Hotspots
[作者：Cannistraro, VJ; Taylor, JS,期刊：Journal of Molecular Biology, 页码：1145-1157 , 文章类型： Article，,卷期：2009年392-5]
Sunlight-induced C -> T mutation hotspots occur most frequently at methylated CpG sites in tumor suppressor genes and are thought to arise from translesion synthesis past deaminated cyclobutane pyrimidine dimers (CPDs). ...

Functional Effects of a Restrictive-Cardiomyopathy-Linked Cardiac Troponin I Mutation (R145W) in Transgenic Mice
[作者：Wen, YH; Xu, YY; Wang, YC; Pinto, JR; Potter, JD; Kerrick, WGL,期刊：Journal of Molecular Biology, 页码：1158-1167 , 文章类型： Article，,卷期：2009年392-5]
The human cardiac troponin I (hcTnI) mutation R145W has been associated with restrictive cardiomyopathy. In this study, simultaneous measurements of ATPase activity and force in skinned papillary fibers from hcTnI R145W ...

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