Effect of Oligosaccharides and their Monosaccharide Mixtures on the Stability of Proteins: A Scaled Particle Study

Abstract Experimental results of RNase-A stabilization by sugar osmolytes show that the change in the Gibbs free energy (Δ G D) associated with the equilibrium, N (native) state ↔ D (denatured) state of the protein in the presence of equimolar mixture of monosaccharides is larger than that of the corresponding oligosaccharides at a given temperature and pH. However, at the molar scale, ΔG D obtained in the presence of an oligosaccharide is much higher as compared with ΔG D obtained using individual monosaccharide. We used scaled particle theory (SPT) to explain these experimental observations. The effective length, called Tolman's length that describes the curvature correlations to a surface area or surface tension and in turn contributes to the change in free energy, is discussed. Tolman's length is higher for corresponding monomer mixture than the oligosaccharide molecules. Based on SPT analysis, a geometrical model is proposed for clustering of monosaccharides in the mixture due to high particle density. The cluster is presumed to have weak interaction among them due to larger hydrodynamic radius than that of the bonded molecules of oligosaccharides.

[1]  Chandler,et al.  Cavity formation and the drying transition in the lennard-jones fluid , 2000, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[2]  A. Cordomí,et al.  Structural Rearrangements of Rhodopsin Subunits in a Dimer Complex: a Molecular Dynamics Simulation Study , 2009, Journal of biomolecular structure & dynamics.

[3]  S. N. Timasheff,et al.  Protein hydration, thermodynamic binding, and preferential hydration. , 2002, Biochemistry.

[4]  Seokmin Shin,et al.  Simulation Studies on the Stabilities of Aggregates Formed by Fibril-Forming Segments of α-Synuclein , 2009, Journal of biomolecular structure & dynamics.

[5]  Hridoy R Bairagya,et al.  An Insight to the Dynamics of Conserved Water Molecular Triad in IMPDH II (Human): Recognition of Cofactor and Substrate to Catalytic Arg 322 , 2009, Journal of biomolecular structure & dynamics.

[6]  B Honig,et al.  Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects. , 1991, Science.

[7]  R. Bhat,et al.  Thermal Stability of Proteins in Aqueous Polyol Solutions: Role of the Surface Tension of Water in the Stabilizing Effect of Polyols , 1998 .

[8]  T. Ghosh,et al.  Structural Interaction Between DsrE-DsrF-DsrH Proteins Involved in the Transport of Electrons in the dsr Operon , 2008, Journal of biomolecular structure & dynamics.

[9]  H. Reiss Scaled Particle Methods in the Statistical Thermodynamics of Fluids , 2007 .

[10]  D. Allen,et al.  Osmolyte-induced changes in protein conformational equilibria. , 2000, Biopolymers.

[11]  P. Debenedetti,et al.  Simultaneous determination of structural and thermodynamic effects of carbohydrate solutes on the thermal stability of ribonuclease A. , 2004, Journal of the American Chemical Society.

[12]  S. Y. Gerlsma,et al.  The effect of polyhydric and monohydric alcohols on the heat-induced reversible denaturation of lysozyme and ribonuclease. , 2009, International journal of peptide and protein research.

[13]  S. N. Timasheff,et al.  The thermodynamic mechanism of protein stabilization by trehalose. , 1997, Biophysical chemistry.

[14]  S. N. Timasheff,et al.  The control of protein stability and association by weak interactions with water: how do solvents affect these processes? , 1993, Annual review of biophysics and biomolecular structure.

[15]  P. Debenedetti,et al.  Stability of proteins in the presence of carbohydrates; experiments and modeling using scaled particle theory. , 2007, Biophysical chemistry.

[16]  Nader Chaparzadeh,et al.  Structural and Dynamical Studies of Humanin in Water and TFE/Water Mixture: A Molecular Dynamics Simulation , 2008, Journal of biomolecular structure & dynamics.

[17]  Hsuan-Liang Liu,et al.  RING Domains Functioning as E3 Ligases Reveal Distinct Structural Features: A Molecular Dynamics Simulation Study , 2008, Journal of biomolecular structure & dynamics.

[18]  R. K. Singh,et al.  Effect of monomeric and oligomeric sugar osmolytes on DeltaGD, the Gibbs energy of stabilization of the protein at different pH values: is the sum effect of monosaccharide individually additive in a mixture? , 2008, Biophysical chemistry.

[19]  Seokmin Shin,et al.  Conformational Characteristics of Unstructured Peptides: α-Synuclein , 2008 .

[20]  Howard Reiss,et al.  Statistical Mechanics of Rigid Spheres , 1959 .

[21]  Seema Mishra Function Prediction of Rv0079, A Hypothetical Mycobacterium tuberculosis DosR Regulon Protein , 2009, Journal of biomolecular structure & dynamics.

[22]  A. Pal,et al.  Three-dimensional Models of NB-ARC Domains of Disease Resistance Proteins in Tomato, Arabidopsis, and Flax , 2008, Journal of biomolecular structure & dynamics.

[23]  B. Chang,et al.  Effects of sucrose on conformational equilibria and fluctuations within the native‐state ensemble of proteins , 2003, Protein science : a publication of the Protein Society.

[24]  Rajaiah Shenbagarathai,et al.  Sequence Analysis, Structure Prediction, and Functional Validation of phaC1/phaC2 Genes of Pseudomonas sp. LDC-25 and Its Importance in Polyhydroxyalkanoate Accumulation , 2009, Journal of biomolecular structure & dynamics.

[25]  L. Pratt,et al.  Colloquium : Scaled particle theory and the length scales of hydrophobicity , 2006 .

[26]  J. Henderson Solvation of a solvophobic sphere , 2002 .

[27]  D. W. Bolen,et al.  Increased thermal stability of proteins in the presence of naturally occurring osmolytes. , 1992, Biochemistry.

[28]  V. Bloomfield,et al.  Excluded volume in solvation: sensitivity of scaled-particle theory to solvent size and density. , 2000, Biophysical journal.

[29]  G. Somero,et al.  Biochemical Adaptation: Mechanism and Process in Physiological Evolution , 1984 .

[30]  D. Erie,et al.  Sugar-induced molten-globule model. , 1998, Biochemistry.

[31]  J. Kirkwood,et al.  The Statistical Mechanical Theory of Solutions. I , 1951 .

[32]  R. Tolman,et al.  The Principles of Statistical Mechanics. By R. C. Tolman. Pp. xix, 661. 40s. 1938. International series of monographs on physics. (Oxford) , 1939, The Mathematical Gazette.

[33]  R. Tolman The Effect of Droplet Size on Surface Tension , 1949 .

[34]  M. E. Clark,et al.  Living with water stress: evolution of osmolyte systems. , 1982, Science.

[35]  R. Veenstra,et al.  Monovalent Ion Selectivity Sequences of the Rat Connexin43 Gap Junction Channel , 1997, The Journal of general physiology.

[36]  Piramanayagam Shanmughavel,et al.  Molecular Modeling of Human Pentameric α7 Neuronal Nicotinic Acetylcholine Receptor and Its Interaction with its Agonist and Competitive Antagonist , 2009, Journal of biomolecular structure & dynamics.

[37]  J. Dasgupta,et al.  Structural Determinants of V. cholerae CheYs that Discriminate them in FliM binding: Comparative Modeling and MD Simulation Studies , 2008, Journal of biomolecular structure & dynamics.

[38]  Joel L. Lebowitz,et al.  Scaled Particle Theory of Fluid Mixtures , 1965 .

[39]  D. Erie,et al.  Interpreting the effects of small uncharged solutes on protein-folding equilibria. , 2001, Annual review of biophysics and biomolecular structure.

[40]  D'Annessa Ilda,et al.  Structural-Dynamical Properties of the Deinococcus Radiodurans Topoisomerase IB in Absence of DNA: Correlation with the Human Enzyme , 2009, Journal of biomolecular structure & dynamics.

[41]  Dinesh Gupta,et al.  Molecular Modeling Studies of the Interaction Between Plasmodium falciparum HslU and HslV Subunits , 2009, Journal of biomolecular structure & dynamics.

[42]  I. Ghosh,et al.  Determination of Phosphorylation Sites for NADP-specific Isocitrate Dehydrogenase from Mycobacterium tuberculosis , 2009, Journal of biomolecular structure & dynamics.

[43]  Bipin G. Nair,et al.  Homology Modeling of GLUT4, an Insulin Regulated Facilitated Glucose Transporter and Docking Studies with ATP and its Inhibitors , 2009, Journal of biomolecular structure & dynamics.

[44]  M. Paulaitis,et al.  Effect of solute size and solute-water attractive interactions on hydration water structure around hydrophobic solutes. , 2001, Journal of the American Chemical Society.

[45]  P. Garriga,et al.  Molecular Dynamics Simulations of Rhodopsin Point Mutants at the Cytoplasmic Side of Helices 3 and 6 , 2008, Journal of biomolecular structure & dynamics.

[46]  D. W. Bolen,et al.  Mixed osmolytes: The degree to which one osmolyte affects the protein stabilizing ability of another , 2006, Protein science : a publication of the Protein Society.

[47]  Jiapu Zhang,et al.  Studies on the Structural Stability of Rabbit Prion Probed by Molecular Dynamics Simulations , 2009, Journal of biomolecular structure & dynamics.

[48]  S J Prestrelski,et al.  Separation of freezing- and drying-induced denaturation of lyophilized proteins using stress-specific stabilization. I. Enzyme activity and calorimetric studies. , 1993, Archives of biochemistry and biophysics.

[49]  Daniela Josa,et al.  Homology Modeling of Wild-type, D516V, and H526L Mycobacterium Tuberculosis RNA Polymerase and Their Molecular Docking Study with Inhibitors , 2008, Journal of biomolecular structure & dynamics.

[50]  Sai Kumar Ramadugu,et al.  Study of Early Events in the Protein Folding of Villin Headpiece using Molecular Dynamics Simulation , 2008, Journal of biomolecular structure & dynamics.

[51]  B. Widom,et al.  Some Topics in the Theory of Fluids , 1963 .

[52]  Sujit Roy,et al.  Sequential, Structural, and Phylogenetic Study of BRCT Module in Plants , 2008, Journal of biomolecular structure & dynamics.

[53]  H. Reiss Statistical geometry in the study of fluids and porous media , 1992 .