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Journal Issue - Volume 16 Issue 10 (October 2007)

Abstract Polyketides are a medicinally important class of natural products. The architecture of modular polyketide synthases (PKSs), composed of multiple covalently linked domains grouped into modules, provides an attractive framework for engineering novel polyketide‐producing assemblies. However, impaired domain–domain interactions can compromise the efficiency of engineered polyketide biosynthesis. To facilitate the study of these...

Abstract The preS1 surface antigen of hepatitis B virus (HBV) is known to play an important role in the initial attachment of HBV to hepatocytes. We have characterized structural features of the full‐length preS1 using heteronuclear NMR methods and discovered that this 119‐residue protein is inherently unstructured without a unique tertiary structure under a nondenaturing condition. Yet, combination of various NMR parameters shows...

Abstract We have tested the role of the polar loop of subunit c of the Escherichia coli ATP synthase in stabilizing the hairpin structure of this protein. The structure of the c32–52 peptide corresponding to the cytoplasmic region of subunit c bound to the dodecylphosphocholine micelles was solved by high‐resolution NMR. The region comprising residues 41–47 forms a well‐ordered structure rather similar to the conformation of the polar loop region in the...

Abstract We developed a series of statistical potentials to recognize the native protein from decoys, particularly when using only a reduced representation in which each side chain is treated as a single Cβ atom. Beginning with a highly successful all‐atom statistical potential, the Discrete Optimized Protein Energy function (DOPE), we considered the implications of including additional information in the all‐atom statistical potential and subsequently ...

Abstract X‐ray crystallographic protein structures often contain disordered regions that are observed as missing electron density. Diffraction data may give little or no direct evidence as to the specific nature of disordered regions. We have developed a weighted window‐based disorder predictor optimized using crystallographic data. Performance of a predictor is strongly influenced by chain termini. Optimized score adjustment values...

Abstract Structural characterization of transmembrane peptides (TMPs) is justified because transmembrane domains of membrane proteins appear to often function independently of the rest of the protein. However, the challenge in obtaining milligrams of isotopically labeled TMPs to study these highly hydrophobic peptides by nuclear magnetic resonance (NMR) is significant. In the present work, a protocol is developed to produce,...

Abstract Previous studies identified several single‐point mutants of the prion protein that displayed dominant‐negative effects on prion replication. The dominant‐negative effect was assumed to be mediated by protein X, an as‐yet‐unknown cellular cofactor that is believed to be essential for prion replication. To gain insight into the mechanism that underlies the dominant‐negative phenomena, we evaluated the effect of the Q218K...

Abstract Human TAG‐1 is a neural cell adhesion molecule that is crucial for the development of the nervous system during embryogenesis. It consists of six immunoglobulin‐like and four fibronectin III‐like domains and is anchored to the membrane by glycosylphosphatidylinositol. Herein we present the crystal structure of the four N‐terminal immunoglobulin‐like domains of TAG‐1 (TAG‐1Ig1–4), known to be important in heterophilic and homophilic...

Abstract Pyridoxal kinase catalyzes the transfer of a phosphate group from ATP to the 5′ alcohol of pyridoxine, pyridoxamine, and pyridoxal. In this work, kinetic studies were conducted to examine monovalent cation dependence of human pyridoxal kinase kinetic parameters. The results show that hPLK affinity for ATP and PL is increased manyfold in the presence of K+ when compared to Na+; however, the maximal activity of the Na+ form of the enzyme...

Abstract Many human proteins contain consecutive amino acid repeats, known as homopolymeric amino acid (HPAA) tracts. Some inherited diseases are caused by proteins in which HPAAs are expanded to an excessive length. To this day, nine polyglutamine‐related diseases and nine polyalanine‐related diseases have been reported, including Huntington's disease and oculopharyngeal muscular dystrophy. In this study, potential HPAA–HPAA...

Abstract The channel‐forming trans‐membrane domain of Vpu (Vpu TM) from HIV‐1 is known to enhance virion release from the infected cells and is a potential target for ion‐channel blockers. The substitution of alanine at position 18 by a histidine (A18H) has been shown to render HIV‐1 infections susceptible to rimantadine, a channel blocker of M2 protein from the influenza virus. In order to describe the influence of the mutation on...

Abstract S/π interactions are prevalent in biochemistry and play an important role in protein folding and stabilization. Geometries of cysteine/aromatic interactions found in crystal structures from the Brookhaven Protein Data Bank (PDB) are analyzed and compared with the equilibrium configurations predicted by high‐level quantum mechanical results for the H2S–benzene complex. A correlation is observed between the energetically favorable...

Abstract The previous design of an unprecedented family of two‐, three‐, and four‐helical, right‐handed coiled coils utilized nonbiological amino acids to efficiently pack spaces in the oligomer cores. Here we show that a stable, right‐handed parallel tetrameric coiled coil, called RH4B, can be designed entirely using biological amino acids. The X‐ray crystal structure of RH4B was determined to 1.1 Å resolution using a designed...

Abstract The folding of WW domains is rate limited by formation of a β‐hairpin comprising residues from strands 1 and 2. Residues in the turn of this hairpin have reported Φ‐values for folding close to 1 and have been proposed to nucleate folding. High Φ‐values do not necessarily imply that the energetics of formation are a driving force for initiating folding. We demonstrate by NMR studies and molecular dynamics simulations that...

Abstract We report the design and engineering of a robust, reagentless fluorescent glucose biosensor based on the periplasmic glucose‐binding protein obtained from Thermotoga maritima (tmGBP). The gene for this protein was cloned from genomic DNA and overexpressed in Escherichia coli, the identity of its cognate sugar was confirmed, ligand binding was studied, and the structure of its glucose complex was solved to 1.7 Å resolution by X‐ray...

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