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Journal Issue - Volume 13 Issue 1 (January 2004)

Abstract It was shown previously that complementation could be a powerful mean to probe protein–protein interactions in the normally tetrameric R67 DHFR. Indeed, mixing complementing inactive dimeric mutants produced active heterotetramers. This approach turned a homo‐oligomer into a hetero‐oligomer and thus allowed the use of combinatorial assays, a subtle analysis of the association forces, and a precise determination of the...

Abstract Shape information about macromolecules is increasingly available but is difficult to use in modeling efforts. We demonstrate that shape information alone can often distinguish structural models of biological macromolecules. By using a data structure called a surface envelope (SE) to represent the shape of the molecule, we propose a method that generates a fitness score for the shape of a particular molecular model. This...

Abstract α and β Tubulin are well‐characterized paralogs with similar structures and functions. We quantify the variability of every amino acid position in both tubulins from the aligned sequences of their numerous known orthologs. By aligning the variability profiles, we identify residues that differ significantly in variability between α and β tubulin. Most of these residues are part of well‐defined secondary structures and are...

Abstract N3 is the third position from the N terminus in the α‐helix with helical backbone dihedral angles. All 20 amino acids have been placed in the N3 position of a synthetic helical peptide (CH3CO‐[AAX AAAAKAAAAKAGY]‐NH2) and the helix content measured by circular dichroism spectroscopy at 273 K. The dependence of peptide helicity on N3 residue identity has been used to determine a free energy scale by analysis with a modified Lifson‐Roig...

Abstract We have performed discontinuous molecular dynamics simulations of the thermodynamics and stability of a tetrameric β‐sheet complex that contains four identical four‐stranded antiparallel β‐sheet peptides. The potential used in the simulation is a hybrid Go‐type potential characterized by the bias gap parameter g, an artificial measure of the preference of a model protein for its native state, and the intermolecular contact parameter ...

Abstract We developed a variant of the intermediate sequence search method (ISSnew) for detection and alignment of weakly similar pairs of protein sequences. ISSnew relates two query sequences by an intermediate sequence that is potentially homologous to both queries. The improvement was achieved by a more robust overlap score for a match between the queries through an intermediate. The approach was benchmarked on a data set of 2369 sequences...

Abstract We describe expression, purification, and characterization of three site‐specific mutants of recombinant human stefin B: H75W, P36G, and P79S. The far‐ and near‐UV CD spectra have shown that they have similar secondary and tertiary structures to the parent protein. The elution on gel‐filtration suggests that recombinant human stefin B and the P36G variant are predominantly monomers, whereas the P79S variant is a dimer. ANS...

  • Protein flexibility and intrinsic disorder

  • Predrag Radivojac, Zoran Obradovic, David K. Smith, Guang Zhu, Slobodan Vucetic, Celeste J. Brown, J. David Lawson, A. Keith Dunker
  • Published in Wiley Interscience on Jan 01, 2009
  • DOI: 10.1110/ps.03128904 (p 71-80)

Abstract Comparisons were made among four categories of protein flexibility: (1) low‐B‐factor ordered regions, (2) high‐B‐factor ordered regions, (3) short disordered regions, and (4) long disordered regions. Amino acid compositions of the four categories were found to be significantly different from each other, with high‐B‐factor ordered and short disordered regions being the most similar pair. The high‐B‐factor (flexible) ordered...

Abstract The pathway for the in vitro equilibrium unfolding of the tubulin heterodimer by guanidinium chloride (GdmCl) has been studied using several spectroscopic techniques, specifically circular dichroism (CD), two‐photon Fluorescence Correlation Spectroscopy (FCS), and time‐resolved fluorescence, including lifetime and dynamic polarization. The results show that tubulin unfolding is characterized by distinct processes that occur...

Abstract Recombinant mesophilic Escherichia coli (Ec) and thermophilic Bacillus stearothermophilus (Bst) elongation factors EF‐Tus, their isolated G‐domains, and six chimeric EF‐Tus composed of domains of either EF‐Tu were prepared, and their GDP/GTP binding activities and thermostability were characterized. BstEF‐Tu and BstG‐domain bound GDP and GTP with affinities in nanomolar and submicromolar ranges, respectively, fully comparable with...

Abstract Analysis of circular dichroism spectra of proteins provides information about protein secondary structure. Analytical methods developed for such an analysis use structures and spectra of a set of reference proteins. The reference protein sets currently in use include soluble proteins with a wide range of secondary structures, and perform quite well in analyzing CD spectra of soluble proteins. The utility of soluble protein...

Abstract The results of minimal model calculations indicate that the stability and the kinetic accessibility of the native state of small globular proteins are controlled by few “hot” sites. By means of molecular dynamics simulations around the native conformation, which describe the protein and the surrounding solvent at the all‐atom level, an accurate and compact energetic map of the native state of the protein is generated. This...

Abstract We expressed and characterized two sHsps, StHsp19.7 and StHsp14.0, from a thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain 7. StHsp19.7 forms a filamentous structure consisting of spherical particles and lacks molecular chaperone activity. Fractionation of Sulfolobus extracts by size exclusion chromatography with immunoblotting indicates that StHsp19.7 exists as a filamentous structure in vivo. On the other hand, StHsp14.0...

Abstract The type II transmembrane serine protease dipeptidyl peptidase IV (DPPIV), also known as CD26 or adenosine deaminase binding protein, is a major regulator of various physiological processes, including immune, inflammatory, nervous, and endocrine functions. It has been generally accepted that glycosylation of DPPIV and of other transmembrane dipeptidyl peptidases is a prerequisite for enzyme activity and correct protein...

Abstract AMP‐activated protein kinase (AMPK) is a αβγ heterotrimer that is activated in response to both hormones and intracellular metabolic stress signals. AMPK is regulated by phosphorylation on the α subunit and by AMP allosteric control previously thought to be mediated by both α and γ subunits. Here we present evidence that adjacent γ subunit pairs of CBS repeat sequences (after Cystathionine Beta Synthase) form an AMP binding...

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