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Journal Issue - Volume 13 Issue 10 (October 2004)

  • The Open Access Debate

  • Mark Hermodson
  • Published in Wiley Interscience on Jan 01, 2009
  • DOI: 10.1002/pro.132569 (p 2569-2570)

  • Anil Lala (1950–2004)

  • P. Balaram
  • Published in Wiley Interscience on Jan 01, 2009
  • DOI: 10.1002/pro.132571 (p 2571-2572)

Abstract The C terminus of the nuclear protein NuMA, NuMA‐CT, has a well‐known function in mitosis via its proximal segment, but it seems also involved in the control of differentiation. To further investigate the structure and function of NuMA, we exploited established computational techniques and tools to collate and characterize proteins with regions similar to the distal portion of NuMA‐CT (NuMA‐CTDP). The phylogenetic...

Abstract The interactions of several affinity reagent displayed T7 and M13 phage particles with their corresponding target molecules were examined using Fluorescence Correlation Spectroscopy (FCS). Diffusion times, relative fractions of each component in the recognition reactions at the equilibrium state, and ultimately the dissociation constants were deduced from analyzing the fluorescence autocorrelation curves. Although the...

Abstract Williams‐Beuren syndrome (WBS) is a neurological disorder resulting from a microdeletion, typically 1.5 megabases in size, at 7q11.23. Atypical patients implicate genes at the telomeric end of this multigene deletion as the main candidates for the pathology of WBS in particular the unequal cognitive profile associated with the condition. We recently identified a gene (GTF2IRD2) that shares homology with other members of a...

Abstract A theoretical approach for estimating association free energies of α‐helices in nonpolar media has been developed. The parameters of energy functions have been derived from ΔΔG values of mutants in water‐soluble proteins and partitioning of organic solutes between water and nonpolar solvents. The proposed approach was verified successfully against three sets of published data: (1) dissociation constants of α‐helical ...

Abstract We present a two‐step approach to modeling the transmembrane spanning helical bundles of integral membrane proteins using only sparse distance constraints, such as those derived from chemical cross‐linking, dipolar EPR and FRET experiments. In Step 1, using an algorithm, we developed, the conformational space of membrane protein folds matching a set of distance constraints is explored to provide initial structures for local...

Abstract The folding of Pseudomonas aeruginosa apo‐azurin was investigated with the intent of identifying putative intermediates. Two apo‐mutants were constructed by replacing the main metal‐binding ligand C112 with a serine (C112S) and an alanine (C112A). The guanidinium‐induced unfolding free energies (ΔGU−NH2O) of the C112S and C112A mutants were measured to 36.8 ± 1 kJ mole−1 and 26.1 ± 1 kJ mole−1, respectively, and the m‐value of the...

Abstract Bikunin is a glycosylated protein that aggregates extensively during mammalian cell culture, resulting in loss of activity, loss of native secondary structure, and the formation of nonnative disulfide bonds. We investigated the use of high hydrostatic pressure (1000–3000 bar) for the refolding of bikunin aggregates. The refolding yield obtained with pressure‐modulated refolding at 2000 bar was 70 (±5%) by reverse‐phase...

Abstract Gene duplication is thought to be a major source of evolutionary innovation because it allows one copy of a gene to mutate and explore genetic space while the other copy continues to fulfill the original function. Models of the process often implicitly assume that a single mutation to the duplicated gene can confer a new selectable property. Yet some protein features, such as disulfide bonds or ligand binding sites, require...

  • Crystallographic identification of Ca 2 B domain

  • Yuan Cheng, Sonia M. Sequeira, Lucy Malinina, Valentina Tereshko, Thomas H. Söllner, Dinshaw J. Patel
  • Published in Wiley Interscience on Jan 01, 2009
  • DOI: 10.1110/ps.04832604 (p 2665-2672)

Abstract Synaptotagmin I has two tandem Ca2+‐binding C2 domains, which are essential for fast synchronous synaptic transmission in the central nervous system. We have solved four crystal structures of the C2B domain, one of them in the cation‐free form at 1.50 Å resolution, two in the Ca2+‐bound form at 1.04 Å (two bound Ca2+ ions) and 1.65 Å (three bound Ca2+ ions) resolution and one in the Sr2+‐bound form at 1.18 Å (one bound Sr2+ ion) resolution. The...

Abstract Ski8p is a WD‐repeat protein with an essential role for the Ski complex assembly in an exosome‐dependent 3′‐to‐5′ mRNA decay. In addition, Ski8p is involved in meiotic recombination by interacting with Spo11p protein. We have determined the crystal structure of Ski8p from Saccharomyces cerevisiae at 2.2 Å resolution. The structure reveals that Ski8p folds into a seven‐bladed β propeller. Mapping sequence conservation and...

Abstract Bovine viral diarrhea virus (BVDV) nonstructural protein 5B is an RNA‐dependent RNA polymerase, essential for viral replication. Initial attempts to crystallize a soluble form of the 695‐residue BVDV polymerase did not produce any crystals. Limited proteolysis, homology modeling, and mutagenesis data were used to aid the design of polymerase constructs that might crystallize more readily. Limited proteolysis of the...

Abstract The accuracy of in vivo incorporation of amino acids during protein biosynthesis is controlled to a significant extent by aminoacyl‐tRNA synthetases (aaRS). This paper describes the application of the HierDock computational method to study the molecular basis of amino acid binding to the Escherichia coli methionyl tRNA synthetase (MetRS). Starting with the protein structure from the MetRS cocrystal, the HierDock calculations ...

Abstract The effects on folding kinetics and equilibrium stability of core mutations in the apo‐mutant C112S of azurin from Pseudomonas aeruginosa were studied. A number of conserved residues within the cupredoxin family were recognized by sequential alignment as constituting a common hydrophobic core: I7, F15, L33, W48, F110, L50, V95, and V31. Of these, I7, V31, L33, and L50 were mutated for the purpose of obtaining information on the...

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