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Molecular Crowding (molecular + crowding)
Selected AbstractsA potential role for isothermal calorimetry in studies of the effects of thermodynamic non-ideality in enzyme-catalyzed reactions,JOURNAL OF MOLECULAR RECOGNITION, Issue 5 2004Thierry G. A. Lonhienne Abstract Attention is drawn to the feasibility of using isothermal calorimetry for the characterization of enzyme reactions under conditions bearing greater relevance to the crowded biological environment, where kinetic parameters are likely to differ significantly from those obtained by classical enzyme kinetic studies in dilute solution. An outline of the application of isothermal calorimetry to the determination of enzyme kinetic parameters is followed by considerations of the nature and consequences of crowding effects in enzyme catalysis. Some of those effects of thermodynamic non-ideality are then illustrated by means of experimental results from calorimetric studies of the effect of molecular crowding on the kinetics of catalysis by rabbit muscle pyruvate kinase. This review concludes with a discussion of the potential of isothermal calorimetry for the experimental determination of kinetic parameters for enzymes either in biological environments or at least in media that should provide reasonable approximations of the crowded conditions encountered in vivo. Copyright © 2004 John Wiley & Sons, Ltd. [source] The effect of macromolecular crowding on protein aggregation and amyloid fibril formation,JOURNAL OF MOLECULAR RECOGNITION, Issue 5 2004Larissa A. Munishkina Abstract Macromolecular crowding is expected to have several significant effects on protein aggregation; the major effects will be those due to excluded volume and increased viscosity. In this report we summarize data demonstrating that macromolecular crowding may lead to a dramatic acceleration in the rate of protein aggregation and formation of amyloid fibrils, using the protein ,-synuclein. The aggregation of ,-synuclein has been implicated as a critical factor in development of Parkinson's disease. Various types of polymers, from neutral polyethylene glycols and polysaccharides (Ficolls, dextrans) to inert proteins, are shown to accelerate ,-synuclein fibrillation. The stimulation of fibrillation increases with increasing length of polymer, as well as increasing polymer concentration. At lower polymer concentrations (typically up to ,100,mg/ml) the major effect is ascribed to excluded volume, whereas at higher polymer concentrations evidence of opposing viscosity effects become apparent. Pesticides and metals, which are linked to increased risk of Parkinson's disease by epidemiological studies, are shown to accelerate ,-synuclein fibrillation under conditions of molecular crowding. Copyright © 2004 John Wiley & Sons, Ltd. [source] Effects of molecular crowding by saccharides on ,-chymotrypsin dimerizationPROTEIN SCIENCE, Issue 5 2002Chetan N. Patel Abstract Given the importance of protein complexes as therapeutic targets, it is necessary to understand the physical chemistry of these interactions under the crowded conditions that exist in cells. We have used sedimentation equilibrium to quantify the enhancement of the reversible homodimerization of ,-chymotrypsin by high concentrations of the osmolytes glucose, sucrose, and raffinose. In an attempt to rationalize the osmolyte-mediated stabilization of the ,-chymotrypsin homodimer, we have used models based on binding interactions (transfer-free energy analysis) and steric interactions (excluded volume theory) to predict the stabilization. Although transfer-free energy analysis predicts reasonably well the relatively small stabilization observed for complex formation between cytochrome c and cytochrome c peroxidase, as well as that between bobtail quail lysozyme and a monoclonal Fab fragment, it underestimates the sugar-mediated stabilization of the ,-chymotrypsin dimer. Although predictions based on excluded volume theory overestimate the stabilization, it would seem that a major determinant in the observed stabilization of the ,-chymotrypsin homodimer is the thermodynamic nonideality arising from molecular crowding by the three small sugars. [source] Effect of short-range forces on the length distribution of fibrous cytoskeletal proteinsBIOPOLYMERS, Issue 9 2008David Popp Abstract The length distribution of cytoskeletal filaments is an important physical parameter, which can modulate physiological cell functions. In both eukaryotic and prokaryotic cells various biological cytoskeletal polymers form supramolecular structures due to short-range forces induced mainly by molecular crowding or cross linking proteins, but their in vivo length distribution remains difficult to measure. In general, based on experimental evidence and mathematical modeling of actin filaments in aqueous solutions, the steady state length distribution of fibrous proteins is believed to be exponential. We performed in vitro TIRF- and electron-microscopy to demonstrate that in the presence of short-range forces, which are an integral part of any living cell, the steady state length distributions of the eukaryotic cytoskeletal biopolymer actin, its prokaryotic homolog ParM and microtubule homolog FtsZ deviate from the classical exponential and are either double-exponential or Gaussian, as recent theoretical modeling predicts. Double exponential or Gaussian distributions opposed to exponential can change for example the visco-elastic properties of actin networks within the cell, influence cell motility by decreasing the amount of free ends at the leading edge of the cell or effect the assembly of FtsZ into the bacterial Z-ring thus modulating membrane constriction. © 2008 Wiley Periodicals, Inc. Biopolymers 89: 711,721, 2008. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Structure and chiroptical properties of supramolecular flower pigmentsCHIRALITY, Issue 2 2006George A. EllestadArticle first published online: 30 DEC 200 Abstract Research over the last 30 years has shown that at physiological concentrations of ca. 5 × 10,3 M, flower pigments composed of anthocyanins, either alone or complexed with flavone copigments, and frequently with metals, are self-assembled into non-covalent, chiral supramolecular complexes. This serves several biological functions including color stability, protection against UV radiation and provision for specific colors to attract insects for pollination. Self-association of the monomers takes place under conditions of molecular crowding by precise matching of the ,,, stacking interactions of the aromatic chromophores and intermolecular hydrogen bonding between the attached sugars. The resulting handedness is controlled by the chiral information provided by the sugars joined glycosidically at certain positions around the periphery of the aromatic nuclei. This review gives an overview of (i) the physicochemical evidence including circular dichroism, 1H NMR, and X-ray analysis for the structure and supramolecular chirality of these amphiphilic complexes, (ii) the role of the sugars on directing the chirality of the resulting supramolecules, (iii) the energetics of monomer association, and (iv) the possible influence of stacking chirality on insect pollination. © 2005 Wiley-Liss, Inc. Chirality 18:134,144, 2006. [source] | ||||||||||