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Journal Issue - Volume 5 Issue 7 (July 1996)

Abstract The interaction between calmodulin (CaM) and peptide M13, its target binding sequence from skeletal muscle myosin light chain kinase, involves predominantly two sets of interactions, between the N‐terminal target residues and the C‐domain of calmodulin, and between the C‐terminal target residues and the N‐domain of calmodulin (Ikura M et al., 1992, Science 256:632–638). Using short synthetic peptides based on the two halves of the...

Abstract Differences in the energetics of amide‐amide and amide‐hydroxyl hydrogen bonds in proteins have been explored from the effect of hydroxyl groups on the structure and dissolution energetics of a series of crystalline cyclic dipeptides. The calorimetrically determined energetics are interpreted in light of the crystal structures of the studied compounds. Our results indicate that the amide‐amide and amide‐hydroxyl hydrogen...

Abstract We have implemented an iterative algorithm for the identification of diagnostic patterns from sets of multiple‐domain proteins, where domains need not be common to all the proteins in the defining set. Our algorithm was applied to sequences gathered using a variety of methods, including BLAST, common keywords, and common E.C. numbers. In all cases, useful diagnostic patterns were obtained, possessing both high sensitivity...

Abstract The cellular and structural properties and binding capabilities of a lipocalin expressed in the early neural plate of Xenopus laevis embryos and the adult choroid plexus have been investigated. It was found that this lipocalin, termed Xlcpll, binds retinal at a nanomolar concentration, retinoic acid in the micromolar range, but does not show binding to retinol. Furthermore, this protein also binds D/L thyroxine. The Xlcpl1 cDNA was...

Abstract Transforming growth factors β belong to a group of cytokines that control cellular proliferation and differentiation. Five isoforms are known that share approximately 75% sequence identity, but exert different biological activities. The structure of TGF‐β3 was solved by X‐ray crystallography and refined to a final R‐factor of 17.5% at 2.0 Å resolution. Comparison with the structure of TGF‐β2 (Schlunegger MP, Grütter MG, 1992, Nature...

Abstract Free energy maps of the binding site are constructed for class I major histocompatibility complex (MHC) proteins, by rotating and translating amino acid probes along the cleft, and performing a side‐chain conformational search at each position. The free energy maps are used to determine favorable residue positions that are then combined to form docked peptide conformations. Because the generic backbone structural motif of...

Abstract Because the N‐ and C‐terminal amino acids of the catalytic (c) polypeptide chains of Escherichia coli aspartate transcarbamoylase (ATCase) are in close proximity to each other, it has been possible to form in vivo five different active ATCase variants in which the terminal regions of the wild‐type c chains are linked in a continuous polypeptide chain and new termini are introduced elsewhere in either of the two structural domains of...

Abstract Based on observations of solubility and folding properties of peptide 33‐mers derived from the β‐sheet domains of platelet factor‐4 (PF4), interleukin‐8 (IL‐8), and growth related protein (Gro‐α), as well as other β‐sheet‐forming peptides, general guidelines have been developed to aid in the design of water soluble, self‐association‐induced β‐sheet‐forming peptides. CD, 1H‐NMR, and pulsed field gradient NMR self‐diffusion...

Abstract The active site of the cAMP‐dependent protein kinase catalytic subunit harbors a cluster of acidic residues —Asp 127, Glu 170, Glu 203, Glu 230, and Asp 241 — that are not conserved throughout the protein kinase family. Based on crystal structures of the catalytic subunit, these amino acids are removed from the site of phosphoryl transfer and are implicated in substrate recognition. Glu 230, the most buried of these acidic...

Abstract Structurally similar but sequentially unrelated proteins have been discovered and rediscovered by many researchers, using a variety of structure comparison tools. For several pairs of such proteins, existing structural alignments obtained from the literature, as well as alignments prepared using several different similarity criteria, are compared with each other. It is shown that, in general, they differ from each other,...

Abstract Alanine insertions into the glycophorin A transmembrane helix are found to disrupt helix‐helix dimerization in a way that is fully consistent with earlier saturation mutagenesis data, suggesting that Ala‐insertion scanning can be used to rapidly map the approximate location of structurally and/or functionally important segments in transmembrane helices.

Abstract Crystals of the tetraheme cytochrome c3 from sulfate‐reducing bacteria Desulfovibrio gigas (Dg) (MW 13 kDa, 111 residues, four heme groups) were obtained and X‐ray diffraction data collected to 1.8 Å resolution. The structure was solved by the method of molecular replacement and the resulting model refined to a conventional R‐factor of 14.9%. The three‐dimensional structure shows many similarities to other known crystal structures of tetraheme c3...

Abstract The serine and cysteine proteinases represent two important classes of enzymes that use a catalytic triad to hydrolyze peptides and esters. The active site of the serine proteinases consists of three key residues, Asp … His … Ser. The hydroxyl group of serine functions as a nucleophile and the imidazole ring of histidine functions as a general acid/general base during catalysis. Similarly, the active site of the cysteine...

Abstract In the course of removing a contaminant from preparations of aminoacyl‐tRNA synthetase complexes, a novel purification method has been developed for the eukaryotic cytoplasmic chaperonin known as TRiC or CCT. This method uses only three steps: ammonium sulfate precipitation, pelleting into a sucrose cushion, and heparin‐agarose chromatography. As judged by electrophoresis, sedimentation, and electron microscopy, the...

  • Conformational stability of apoflavodoxin

  • Carlos G. Genzor, Carlos Gómez‐Moreno, Javier Sancho, Alejandro Beldarraín, José Luis López‐Lacomba, Manuel Cortijo
  • Published in Wiley Interscience on Dec 31, 2008
  • DOI: 10.1002/pro.5560050716 (p 1376-1388)

Abstract Flavodoxins are α/β proteins that mediate electron transfer reactions. The conformational stability of apoflavodoxin from Anabœna PCC 7119 has been studied by calorimetry and urea denaturation as a function of pH and ionic strength. At pH > 12, the protein is unfolded. Between pH 11 and pH 6, the apoprotein is folded properly as judged from near‐ultraviolet (UV) circular dichroism (CD) and high‐field 1H NMR spectra. In this pH...

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