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Journal Issue - Volume 16 Issue 8 (August 2007)

Abstract We have been analyzing the extent to which protein secondary structure determines protein tertiary structure in simple protein folds. An earlier paper demonstrated that three‐dimensional structure can be obtained successfully using only highly approximate backbone torsion angles for every residue. Here, the initial information is further diluted by introducing a realistic degree of experimental uncertainty into this...

Abstract S‐Transnitrosation is an important bioregulatory process whereby NO+ equivalents are transferred between S‐nitrosothiols and Cys of target proteins. This reaction proceeds through a common intermediate R–S–N(O−)–S–R′ and it has been proposed that products different from S‐nitrosothiols may be formed in protein cavities. Recently, we have reported on the formation of such a product, an N‐thiosulfoximide, at the active site of the Cys hydrolase...

Abstract A method to rapidly screen libraries of cyclic peptides in vivo for molecules with biological activity has been developed and used to isolate cyclic peptide inhibitors of the ClpXP protease. Fluorescence activated cell sorting was used in conjunction with a fluorescent reporter to isolate cyclic peptides that inhibit the proteolysis of tmRNA‐tagged proteins in Escherichia coli. Inhibitors shared little sequence similarity and...

Abstract FtsZ has two domains, the amino GTPase domain with a Rossmann fold, and the carboxyl domain that resembles the chorismate mutase fold. Bioinformatics analyses suggest that the interdomain interaction is stronger than the interaction of the protofilament longitudinal interfaces. Crystal B factor analysis of FtsZ and detected conformational changes suggest a connection between these domains. The unfolding/folding...

Abstract In this study, we address the problem of local quality assessment in homology models. As a prerequisite for the evaluation of methods for predicting local model quality, we first examine the problem of measuring local structural similarities between a model and the corresponding native structure. Several local geometric similarity measures are evaluated. Two methods based on structural superposition are found to best...

Abstract Growing well‐diffracting crystals constitutes a serious bottleneck in structural biology. A recently proposed crystallization methodology for “stubborn crystallizers” is to engineer surface sequence variants designed to form intermolecular contacts that could support a crystal lattice. This approach relies on the concept of surface entropy reduction (SER), i.e., the replacement of clusters of flexible, solvent‐exposed...

  • Solution structure of the zinc finger HIT domain in protein FON

  • Fahu He, Takashi Umehara, Kengo Tsuda, Makoto Inoue, Takanori Kigawa, Takayoshi Matsuda, Takashi Yabuki, Masaaki Aoki, Eiko Seki, Takaho Terada, Mikako Shirouzu, Akiko Tanaka, Sumio Sugano, Yutaka Muto, Shigeyuki Yokoyama
  • Published in Wiley Interscience on Jan 02, 2009
  • DOI: 10.1110/ps.062635107 (p 1577-1587)

Abstract The zinc finger HIT domain is a sequence motif found in many proteins, including thyroid hormone receptor interacting protein 3 (TRIP‐3), which is possibly involved in maturity‐onset diabetes of the young (MODY). Novel zinc finger motifs are suggested to play important roles in gene regulation and chromatin remodeling. Here, we determined the high‐resolution solution structure of the zinc finger HIT domain in ZNHIT2...

Abstract The crystal structure of the Thermotoga maritima gene product TM0269, determined as part of genome‐wide structural coverage of T. maritima by the Joint Center for Structural Genomics, revealed structural homology with the fourth module of the cobalamin‐dependent methionine synthase (MetH) from Escherichia coli, despite the lack of significant sequence homology. The gene specifying TM0269 lies in close proximity to another gene, TM0268, ...

Abstract The monomeric Alzheimer's β amyloid peptide, Aβ, is known to adopt a disordered state in water at room temperature, and a circular dichroism (CD) spectroscopy experiment has provided the secondary‐structure contents for the disordered state: 70% random, 25% β‐structural, and 5% helical. We performed an enhanced conformational sampling (multicanonical molecular dynamics simulation) of a 25‐residue segment (residues 12–36) of...

Abstract The burial of nonpolar surface area is known to enhance markedly the conformational stability of proteins. The contribution from the burial of polar surface area is less clear. Here, we report on the tolerance to substitution of Ser75 of bovine pancreatic ribonuclease (RNase A), a residue that has the unusual attributes of being buried, conserved, and polar. To identify variants that retain biological function, we used a...

Abstract The frontline tuberculosis drug isoniazid (INH) inhibits InhA, the NADH‐dependent fatty acid biosynthesis (FAS‐II) enoyl reductase from Mycobacterium tuberculosis (MTB), via formation of a covalent adduct with NAD+ (the INH‐NAD adduct). Resistance to INH can be correlated with many mutations in MTB, some of which are localized in the InhA cofactor binding site. While the InhA mutations cause a substantial decrease in the affinity of...

  • The structure of receptor‐associated protein (RAP)

  • Donghan Lee, Joseph D. Walsh, Molly Migliorini, Ping Yu, Tao Cai, Charles D. Schwieters, Susan Krueger, Dudley K. Strickland, Yun‐Xing Wang
  • Published in Wiley Interscience on Jan 02, 2009
  • DOI: 10.1110/ps.072865407 (p 1628-1640)

Abstract The receptor‐associated protein (RAP) is a molecular chaperone that binds tightly to certain newly synthesized LDL receptor family members in the endoplasmic reticulum (ER) and facilitates their delivery to the Golgi. We have adopted a divide‐and‐conquer strategy to solve the structures of the individual domains of RAP using NMR spectroscopy. We present here the newly determined structure of domain 2. Based on this...

Abstract The different types of naturally occurring, normal human hemoglobins vary in their tetramer–dimer subunit interface strengths (stabilities) by three orders of magnitude in the liganded (CO or oxy) state. The presence of embryonic ζ‐subunits leads to an average 20‐fold weakening of tetramer–dimer interfaces compared to corresponding hemoglobins containing adult α‐subunits. The dimer–monomer interfaces of these hemoglobins...

Abstract Plasminogen activator inhibitor‐1 (PAI‐1) belongs to the serine protease inhibitor (serpin) protein superfamily. Serpins are unique in that their native forms are not the most thermodynamically stable conformation; instead, a more stable, latent conformation exists. During the transition to the latent form, the first strand of β‐sheet C (s1C) in the serpin is peeled away from the β‐sheet, and the reactive center loop (RCL)...

Abstract The homochirality, or isotacticity, of the natural amino acids facilitates the formation of regular secondary structures such as α‐helices and β‐sheets. However, many examples exist in nature where novel polypeptide topologies use both l‐ and d‐amino acids. In this study, we explore how stereochemistry of the polypeptide backbone influences basic properties such as compactness and the size of fold space by simulating both lattice and...

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