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Journal Issue - Volume 2 Issue 11 (November 1993)

  • The name game

  • Ralph A. Bradshaw, Daniel Birnbaum
  • Published in Wiley Interscience on Dec 31, 2008
  • DOI: 10.1002/pro.5560021101 (p 1783-1784)

Abstract We describe how to build protein models from structural templates. Methods to identify structural similarities between proteins in cases of significant, moderate to low, or virtually absent sequence similarity are discussed. The detection and evaluation of structural relationships is emphasized as a central aspect of protein modeling, distinct from the more technical aspects of model building. Computational techniques to...

Abstract Although it is known that three‐dimensional structure is well conserved during the evolutionary development of proteins, there have been few studies that consider other parameters apart from divergence of the main‐chain coordinates. In this study, we align the structures of 90 pairs of homologous proteins having sequence identities ranging from 5 to 100%. Their structures are compared as a function of sequence identity,...

Abstract We introduce a method for docking small flexible ligands of the size of dipeptides and phosphocholine and test it against crystallographic complexes. We then show how the method can be used as the basis for a strategy for solving the much more difficult problem of docking fully flexible peptides in the 8–10‐residue size range. After developing the method we apply it to peptide–MHC class I systems and find that the...

Abstract Single tryptophan mutants of the trp aporepressor, tryptophan 19 → phenylalanine (W19F) and tryptophan 99 → phenylalanine (W99F), were used in this study to resolve the individual steady‐state and time‐resolved fluorescence urea unfolding profiles of the two tryptophan residues in this highly intertwined, dimeric protein. The wild‐type protein exhibits a large increase in fluorescence intensity and lifetime, as well as a...

Abstract Mutants of the dimeric Escherichia coli trp aporepressor are constructed by replacement of the two tryptophan residues in each subunit in order to assess the effects on equilibrium and kinetic fluorescence properties of the folding reaction. The three kinetic phases detected by intrinsic tryptophan fluorescence in refolding of the wild‐type aporepressor are also observed in folding of both Trp 19 to Phe and Trp 99 to Phe...

Abstract A core‐glycosylated form of the dimeric enzyme invertase has been isolated from secretion mutants of Saccharomyces cerevisiae blocked in transport to the Golgi apparatus. This glycosylation variant corresponds to the form that folds and associates during biosynthesis of the protein in vivo. In the present work, its largely homogeneous subunit size and well‐defined quaternary structure were utilized to characterize the folding and...

Abstract Temperature‐sensitive folding (tsf) and global‐tsf‐suppressor (su) point mutations affect the folding yields of the trimeric, thermostable phage P22 tailspike endorhamnosidase at elevated temperature, both in vivo and in vitro, but they have little effect on function and stability of the native folded protein. To delineate the mechanism by which these mutations modify the partitioning between productive folding and off‐pathway...

Abstract The morphology of small molecule crystals provides a model for evaluating surface solvation energies in a system with similar packing density to that observed for amino acid residues in proteins. The solvation energies associated with the transfer of methylene and carboxyl groups between vacuum and aqueous phases are estimated to be approx. +40 and ‐260 cal/Å2, respectively, from an analysis of the morphology of succinic acid crystals....

Abstract Sequences of 16 NAD and/or NADP‐linked aldehyde oxidoreductases are aligned, including representative examples of all aldehyde dehydrogenase forms with wide substrate preferences as well as additional types with distinct specificities for certain metabolic aldehyde intermediates, particularly semialdehydes, yielding pairwise identities from 15 to 83%. Eleven of 23 invariant residues are glycine and three are proline,...

Abstract Cytochrome b2 is synthesized as a precursor in the cytoplasm and imported to the intermembrane space of yeast mitochondria. We show here that the precursor contains a tightly folded heme‐binding domain and that translocation of this domain across the outer membrane requires ATP. Surprisingly, it is ATP in the mitochondrial matrix rather than external ATP that drives import of the heme‐binding domain. When the folded...

Abstract To identify sequence‐specific motifs associated with the formation of an ionic pore, we systematically evaluated the channel‐forming activity of synthetic peptides with sequence of predicted transmembrane segments of the voltage‐gated calcium channel. The amino acid sequence of voltage‐gated, dihydropyridine (DHP)‐sensitive calcium channels suggests the presence in each of four homologous repeats (I–IV) of six segments...

Abstract A 22‐residue synthetic peptide encompassing the calmodulin (CaM)‐binding domain of skeletal muscle myosin light chain kinase was studied by two‐dimensional NMR and CD spectroscopy. In water the peptide does not form any regular structure; however, addition of the helix‐inducing solvent trifluoroethanol (TFE) causes it to form an α‐helical structure. The proton NMR spectra of this peptide in 25% and 40% TFE were assigned by double...

  • A escherichia coli

  • Zhen‐Yu Sun, Hoai‐Thu N. Truong, E. A. Pratt, David C. Sutherland, Christine E. Kulig, Ronald J. Homer, Stefan M. Groetsch, Priscilla Y. Hsue, Chien Ho
  • Published in Wiley Interscience on Dec 31, 2008
  • DOI: 10.1002/pro.5560021115 (p 1938-1947)

Abstract d‐Lactate dehydrogenase (d‐LDH) is a membrane‐associated respiratory enzyme of Escherichia coli. The protein is composed of 571 amino acid residues with a flavin adenine dinucleotide (FAD) cofactor, has a molecular weight of approximately 65, 000, and requires lipids or detergents for full activity. We used NMR spectroscopy to investigate the structure of d‐LDH and its interaction with phospholipids. We incorporated 5‐fluorotryptophan...

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