Structural Determinants of a Typical Leucine-Rich Repeat Protein

The structural and functional description of protein-protein complexes and their comprehension is a key concept, not only to increase the scientific knowledge in basic terms but also for the application to the biomedical and pharmaceutical industry. The binding association between proteins is nowadays attribute to a few key residues at the interface - the hot-spots. The complex between the RNase inhibitor (RI) and RNaseA protein provides an excellent system to study the role of the functional epi- tope as it is essential in various molecular recognition processes and constitute one of the tightest complexes known. An energetic pattern of the interface is accomplished by computational alanine scanning mutagenesis and a dynamical characterization is accomplished by a detailed study of the molecular dynamical simulations. A spe- cial emphasis is given to the role of solvation across the interface and the shielding of warm- and hot-spots from water.

[1]  Irina S. Moreira,et al.  Hot spot computational identification: Application to the complex formed between the hen egg white lysozyme (HEL) and the antibody HyHEL-10† , 2007 .

[2]  Xing-Ming Zhao,et al.  APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility , 2010, BMC Bioinformatics.

[3]  D. Case,et al.  Exploring protein native states and large‐scale conformational changes with a modified generalized born model , 2004, Proteins.

[4]  Mainak Guharoy,et al.  Empirical estimation of the energetic contribution of individual interface residues in structures of protein–protein complexes , 2009, J. Comput. Aided Mol. Des..

[5]  Irina S. Moreira,et al.  Accuracy of the numerical solution of the Poisson–Boltzmann equation , 2005 .

[6]  R. Nussinov,et al.  Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues. , 2005, Journal of molecular biology.

[7]  A M Lesk,et al.  Interior and surface of monomeric proteins. , 1987, Journal of molecular biology.

[8]  J Deisenhofer,et al.  Mechanism of ribonuclease inhibition by ribonuclease inhibitor protein based on the crystal structure of its complex with ribonuclease A. , 1996, Journal of molecular biology.

[9]  Julie C. Mitchell,et al.  KFC Server: interactive forecasting of protein interaction hot spots , 2008, Nucleic Acids Res..

[10]  Ozlem Keskin,et al.  Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy , 2009, Bioinform..

[11]  B. Brooks,et al.  Langevin dynamics of peptides: The frictional dependence of isomerization rates of N‐acetylalanyl‐N′‐methylamide , 1992, Biopolymers.

[12]  P. Kollman,et al.  Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. , 2000, Accounts of chemical research.

[13]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[14]  Irina S. Moreira,et al.  Protein–protein recognition: a computational mutagenesis study of the MDM2–P53 complex , 2008 .

[15]  Emil Alexov,et al.  Rapid grid‐based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects , 2002, J. Comput. Chem..

[16]  Cyrus Chothia,et al.  The accessible surface area and stability of oligomeric proteins , 1987, Nature.

[17]  Julie C. Mitchell,et al.  An automated decision‐tree approach to predicting protein interaction hot spots , 2007, Proteins.

[18]  P. Kollman,et al.  A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .

[19]  R Shapiro,et al.  Site-specific mutagenesis reveals differences in the structural bases for tight binding of RNase inhibitor to angiogenin and RNase A. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[20]  Barry Honig,et al.  Extending the Applicability of the Nonlinear Poisson−Boltzmann Equation: Multiple Dielectric Constants and Multivalent Ions† , 2001 .

[21]  F. Cohen,et al.  Structure from function: screening structural models with functional data. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[22]  M. L. Connolly.  Analytical molecular surface calculation , 1983 .

[23]  L Wang,et al.  Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[24]  R Shapiro,et al.  Superadditive and subadditive effects of "hot spot" mutations within the interfaces of placental ribonuclease inhibitor with angiogenin and ribonuclease A. , 1999, Biochemistry.

[25]  P A Fernandes,et al.  Detailed microscopic study of the full zipA:FtsZ interface , 2006, Proteins.

[26]  Peter A. Kollman,et al.  Computational alanine scanning of the 1:1 human growth hormone–receptor complex , 2002, J. Comput. Chem..

[27]  Irina S. Moreira,et al.  Unravelling Hot Spots: a comprehensive computational mutagenesis study , 2006 .

[28]  Pedro A Fernandes,et al.  Hot spot occlusion from bulk water: a comprehensive study of the complex between the lysozyme HEL and the antibody FVD1.3. , 2007, The journal of physical chemistry. B.

[29]  J. Deisenhofer,et al.  A structural basis of the interactions between leucine-rich repeats and protein ligands , 1995, Nature.

[30]  Richard T. Bradshaw,et al.  Comparing experimental and computational alanine scanning techniques for probing a prototypical protein-protein interaction. , 2011, Protein engineering, design & selection : PEDS.

[31]  Pedro A Fernandes,et al.  Backbone Importance for Protein-Protein Binding. , 2007, Journal of chemical theory and computation.

[32]  T. Clackson,et al.  A hot spot of binding energy in a hormone-receptor interface , 1995, Science.

[33]  C. Fraser,et al.  Alanine scanning mutagenesis of conserved arginine/lysine-arginine/lysine-X-X-arginine/lysine G protein-activating motifs on m1 muscarinic acetylcholine receptors. , 1996, Molecular pharmacology.

[34]  Jinyan Li,et al.  Protein binding hot spots and the residue-residue pairing preference: a water exclusion perspective , 2010, BMC Bioinformatics.

[35]  R. Skeel,et al.  Langevin stabilization of molecular dynamics , 2001 .

[36]  Pedro A Fernandes,et al.  Hot spots—A review of the protein–protein interface determinant amino‐acid residues , 2007, Proteins.

[37]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[38]  Pedro Alexandrino Fernandes,et al.  Computational alanine scanning mutagenesis—An improved methodological approach , 2007, J. Comput. Chem..

[39]  Nathan A. Baker,et al.  PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations , 2004, Nucleic Acids Res..

[40]  K. Sharp,et al.  Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models , 1994 .

[41]  R Shapiro,et al.  Analysis of the interactions of human ribonuclease inhibitor with angiogenin and ribonuclease A by mutagenesis: importance of inhibitor residues inside versus outside the C-terminal "hot spot". , 2000, Journal of molecular biology.

[42]  I. Moreira,et al.  COMPUTATIONAL DETERMINATION OF THE RELATIVE FREE ENERGY OF BINDING - APPLICATION TO ALANINE SCANNING MUTAGENESIS , 2007 .

[43]  I. Moreira,et al.  Unraveling the importance of protein-protein interaction: application of a computational alanine-scanning mutagenesis to the study of the IgG1 streptococcal protein G (C2 fragment) complex. , 2006, The journal of physical chemistry. B.

[44]  D. Case,et al.  Theory and applications of the generalized born solvation model in macromolecular simulations , 2000, Biopolymers.

[45]  Doheon Lee,et al.  A feature-based approach to modeling protein–protein interaction hot spots , 2009, Nucleic acids research.

[46]  G. Ciccotti,et al.  Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .