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Journal Issue - Volume 13 Issue 11 (November 2004)

Abstract Human coactosin‐like protein (CLP) shares high homology with coactosin, a filamentous (F)‐actin binding protein, and interacts with 5LO and F‐actin. As a tumor antigen, CLP is overexpressed in tumor tissue cells or cell lines, and the encoded epitopes can be recognized by cellular and humoral immune systems. To gain a better understanding of its various functions and interactions with related proteins, the crystal structure...

Abstract α‐Synuclein is the main component of the intracellular protein aggregates in neurons of patients with Parkinson's disease. The occurrence of the disease is associated with oxidative damage. Although it is known that peroxidative chemistry leads to the aggregation of α‐synuclein in vitro, the specific amino acid types of α‐synuclein involved in this type of aggregation have not been identified. We show, using human...

Abstract Given the sequence of a protein, how can we predict whether it is an enzyme or a non‐enzyme? If it is, what enzyme family class it belongs to? Because these questions are closely relevant to the biological function of a protein and its acting object, their importance is self‐evident. Particularly with the explosion of protein sequences entering into data banks and the relatively much slower progress in using biochemical...

Abstract Ankyrin repeats (AR) are 33‐residue motifs containing a β‐turn, followed by two α‐helices connected by a loop. AR occur in tandem arrangements and stack side‐by‐side to form elongated domains involved in very different cellular tasks. Recently, consensus libraries of AR repeats were constructed. Protein E1_5 represents a member of the shortest library, and consists of only a single consensus repeat flanked by designed N‐...

  • To be folded or to be unfolded?

  • Sergiy O. Garbuzynskiy, Michail Yu. Lobanov, Oxana V. Galzitskaya
  • Published in Wiley Interscience on Dec 29, 2008
  • DOI: 10.1110/ps.04881304 (p 2871-2877)

Abstract The lack of ordered structure in “natively unfolded” proteins raises a general question: Are there intrinsic properties of amino acid residues that are responsible for the absence of fixed structure at physiological conditions? In this article, we demonstrate that the competence of a protein to be folded or to be unfolded may be determined by the property of amino acid residues to form a sufficient number of contacts in a...

Abstract The interactions between the N‐terminal domain of the ε (ε186) and θ subunits of DNA polymerase III of Escherichia coli were investigated using electrospray ionization mass spectrometry. The ε186–θ complex was stable in 9 M ammonium actetate (pH 8), suggesting that hydrophobic interactions have a predominant contribution to the stability of the complex. Addition of primary alkanols to ε186–θ in 0.1 M ammonium acetate (pH 8), led to...

Abstract Aggregation of β‐amyloid (Aβ) into fibrillar deposits is widely believed to initiate a cascade of adverse biological responses associated with Alzheimer's disease. Although it was once assumed that the mature fibril was the toxic form of Aβ, recent evidence supports the hypothesis that Aβ oligomers, intermediates in the fibrillogenic pathway, are the dominant toxic species. In this work we used urea to reduce the driving...

Abstract Under native conditions, apocytochrome b5 exhibits a stable core and a disordered heme‐binding region that refolds upon association with the cofactor. The termini of this flexible region are in close proximity, suggesting that loop closure may contribute to the thermodynamic properties of the apocytochrome. A chimeric protein containing 43 residues encompassing the cytochrome loop was constructed using the cyanobacterial...

Abstract We have investigated the folding of polyalanine by combining discontinuous molecular dynamics simulation with our newly developed off‐lattice intermediate‐resolution protein model. The thermodynamics of a system containing a single Ac‐KA14K‐NH2 molecule has been explored by using the replica exchange simulation method to map out the conformational transitions as a function of temperature. We have also explored the influence of solvent...

Abstract Pineal hormone melatonin (N‐acetyl‐5‐methoxytryptamine) is thought to modulate the calcium/calmodulin signaling pathway either by changing intracellular Ca2+ concentration via activation of its G‐protein–coupled membrane receptors, or through a direct interaction with calmodulin (CaM). The present work studies the direct interaction of melatonin with intact calcium‐saturated CaM both experimentally, by fluorescence and...

Abstract The position dependence of the 13C chemical shifts was investigated at the density functional level for α‐helical model peptides represented by the sequence Ac‐(Ala)i‐X‐(Ala)j‐NH2, where X represents any of the 20 naturally occurring amino acids, with 0 ≤ i ≤ 8 and i + j = 8. Adoption of the locally dense basis approach for the quantum chemical calculations enabled us to reduce the length of the chemical‐shift calculations while ...

Abstract The molten globule (MG) state can be an intermediate in the protein folding pathway; thus, its detailed description can help understanding protein folding. Sodium dodecyl sulfate (SDS), an anionic surfactant that is commonly used to mimic hydrophobic binding environments such as cell membranes, is known to denature some native state proteins, including horse cytochrome c (cyt c). In this article, refolding of acid denatured...

Abstract The self‐association equilibrium of a tracer protein, apomyoglobin (apoMb), in highly concentrated crowded solutions of ribonuclease A (RNase A) and human serum albumin (HSA), has been studied as a model system of protein interactions that occur in crowded macromolecular environments. The rotational diffusion of the tracer protein labeled with two different fluorescent dyes, 8‐anilinonaphthalene‐1‐sulfonate and fluorescein...

Abstract We have engineered a recombinant form of the major bee venom allergen (Api m 1) with the final goal of reducing its IgE reactivity. This molecule (Api mut) contains 24 mutations and one deletion of 10 amino acids. The successive introduction of these sequence modifications led to a progressive loss of specific IgE and IgG reactivity and did not reveal any immunodominant epitopes. However, Api mut exhibited a clear loss of...

Abstract Glutamate synthase (GltS) is a complex iron–sulfur flavoprotein that catalyzes the reductive transfer of L‐glutamine amide group to the C2 carbon of 2‐oxoglutarate yielding two molecules of L‐glutamate. Molecular dynamics calculations in explicit solvent were carried out to gain insight into the conformational flexibility of GltS and into the role played by the enzyme substrates in regulating the catalytic cycle. We have...

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