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Journal Issue - Volume 13 Issue 8 (August 2004)

Abstract Molecular dynamics (MD) simulations have been carried out to study the enzymatic mechanisms of quinoproteins, methanol dehydrogenase (MDH), and soluble glucose dehydrogenase (sGDH). The mechanisms of reduction of the orthoquinone cofactor (PQQ) of MDH and sGDH involve concerted base‐catalyzed proton abstraction from the hydroxyl moiety of methanol or from the 1‐hydroxyl of glucose, and hydride equivalent transfer from the...

Abstract Caspases, a unique family of cysteine proteases, execute programmed cell death (apoptosis). Caspases exist as inactive zymogens in cells and undergo a cascade of catalytic activation at the onset of apoptosis. The activated caspases are subject to inhibition by the inhibitor‐of‐apoptosis (IAP) family of proteins. This inhibition can be effectively removed by diverse proteins that share an IAP‐binding tetrapeptide motif....

Abstract Hunter‐killer peptides are chimeric synthetic peptides that selectively target specific cell types for an apoptotic death. These peptides, which are models for potential therapeutics, contain a homing sequence for receptor‐mediated interactions and a pro‐apoptotic sequence. Homing domains have been designed to target angiogenic tumor cells, prostate cells, arthritic tissue and, most recently, adipose tissue. After a...

Abstract A model for the human δ opioid receptor has been generated via sequence alignment, structure building using the crystal structure of bovine rhodopsin as a template, and refinement by molecular dynamics simulation. The model building suggested that, in addition to the previously postulated interaction between D128 and Y308, an internal salt bridge also exists between residues D128 and R192, both of which are conserved in all...

Abstract Formamidopyrimidine‐DNA glycosylase (Fpg) identifies and removes 8‐oxoguanine from DNA. All of the X‐ray structures of Fpg complexed to an abasic site containing DNA exhibit a common disordered region present in the C‐terminal domain of the enzyme. However, this region is believed to be involved in the damaged base binding site when the initial protein/DNA complex is formed. The dynamic behavior of the disordered...

Abstract CXCL11 (ITAC) is one of three chemokines known to bind the receptor CXCR3, the two others being CXCL9 (Mig) and CXCL10 (IP‐10). CXCL11 differs from the other CXCR3 ligands in both the strength and the particularities of its receptor interactions: It has a higher affinity, is a stronger agonist, and behaves differently when critical N‐terminal residues are deleted. The structure of CXCL11 was determined using solution NMR to...

Abstract A model structure of the Hsc70/auxilin complex has been constructed to gain insight into interprotein substrate transfer and ATP hydrolysis induced conformational changes in the multidomain Hsc70 structure. The Hsc70/auxilin system, which is a member of the Hsp70/Hsp40 chaperone system family, uncoats clathrin‐coated vesicles in an ATP hydrolysis‐driven process. Incorporating previous results from NMR and mutant binding...

Abstract We report a detailed classification of disulfide patterns to further understand the role of disulfides in protein structure and function. The classification is applied to a unique searchable database of disulfide patterns derived from the SwissProt and Pfam databases. The disulfide database contains seven times the number of publicly available disulfide annotations. Each disulfide pattern in the database captures the...

Abstract Amino acid residues associated with functional specificity of cyclin‐dependent kinases (CDKs), mitogen‐activated protein kinases (MAPKs), glycogen synthase kinases (GSKs), and CDK‐like kinases (CLKs), which are collectively termed the CMGC group, were identified by categorizing and quantifying the selective constraints acting upon these proteins during evolution. Many constraints specific to CMGC kinases correspond to...

Abstract Affibodies are a novel class of binding proteins selected from phagemid libraries of the Z domain from staphylococcal protein A. The ZSPA‐1 affibody was selected as a binder to protein A, and it binds the parental Z domain with micromolar affinity. In earlier work we determined the structure of the Z:ZSPA‐1 complex and noted that ZSPA‐1 in the free state exhibits several properties characteristic of a molten globule. Here we present a...

Abstract The HIV‐1 Gag polyprotein contains a segment called p2, located between the capsid (CA) and nucleocapsid (NC) domains, that is essential for ordered virus assembly and infectivity. We subcloned, overexpressed, and purified a 156‐residue polypeptide that contains the C‐terminal capsid subdomain (CACTD) through the NC domain of Gag (CACTD‐p2‐NC, Gag residues 276–431) for NMR relaxation and sedimentation equilibrium (SE) studies. The...

Abstract Dehydroquinate synthase (DHQS) is the N‐terminal domain of the pentafunctional AROM protein that catalyses steps 2 to 7 in the shikimate pathway in microbial eukaryotes. DHQS converts 3‐deoxy‐D‐arabino‐heptulosonate‐7‐phosphate (DAHP) to dehydroquinate in a reaction that includes alcohol oxidation, phosphate β‐elimination, carbonyl reduction, ring opening, and intramolecular aldol condensation. Kinetic analysis of the isolated DHQS...

Abstract H‐bonding between protein surface polar/charged groups and water is one of the key factors of protein hydration. Here, we introduce an Accessible Surface Area (ASA) model for computationally efficient estimation of a free energy of water–protein H‐bonding at any given protein conformation. The free energy of water–protein H‐bonds is estimated using empirical formulas describing probabilities of hydrogen bond formation that...

Abstract The α‐D‐phosphohexomutase superfamily is composed of four related enzymes that catalyze a reversible, intramolecular phosphoryl transfer on their sugar substrates. The enzymes in this superfamily play important and diverse roles in carbohydrate metabolism in organisms from bacteria to humans. Recent structural and mechanistic studies of one member of this superfamily, phosphomannomutase/phosphoglucomutase (PMM/PGM) from...

Abstract Molecular machines order and disorder polypeptides as they form and dissolve large intermolecular interfaces, but the biological significance of coupled ordering and binding has been established in few, if any, macromolecular systems. The ordering and binding of GroES co‐chaperonin mobile loops accompany an ATP‐dependent conformational change in the GroEL chaperonin that promotes client protein folding. Following ATP...

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