Arc-repressor dimerization on DNA: folding rate enhancement by colocalization.

Multimeric proteins are ubiquitous in many cellular processes that require high levels of regulation. Eukaryotic gene expression is often regulated by a mechanism of combinatorial control that involves the binding of dimeric transcription factors to DNA together with the coordinated activity of additional proteins. In this study, we investigated the dimerization of the Arc-repressor on DNA with the aim of achieving microscopic insight into the possible advantages of interacting with DNA as a complex rather than as a monomeric single-domain protein. We used a computational coarse-grained model in which the protein dynamics was governed by native interactions and protein-DNA interactions were dictated by electrostatic forces. Inspired by previous experimental work that showed an enhanced refolding rate for the Arc-repressor in the presence of DNA and other polyanions, we focused on the mechanism and kinetics of the assembly of Arc monomers in the presence of single- (ssDNA) and double-stranded DNA (dsDNA) molecules in a low-salt concentration environment. The electrostatic interactions that attract the protein to the dsDNA were shown to be fundamental in colocalizing the unfolded Arc chains and in accelerating refolding. Arc monomers bind the dsDNA efficiently and nonspecifically, and search for each other via one-dimensional diffusion. The fastest folding of Arc is observed for DNA of 30 bp. Longer DNA is significantly less efficient in accelerating the Arc refolding rate, since the two subunits search distinct regions of the one-dimensional DNA and are therefore much less colocalized. The probability that the two unfolded chains will meet on 200 bp DNA is similar to that in the bulk. The colocalization of Arc subunits on ssDNA results in much faster folding compared to that obtained on dsDNA of the same length. Differences in the rate of Arc refolding, cooperativity, and the structure of its transition state ensemble introduced by ssDNA and dsDNA molecules demonstrate the important role of colocalization in biological self-assembly processes.

[1]  R. Sauer,et al.  DNA recognition by beta-sheets in the Arc repressor-operator crystal structure. , 1994, Nature.

[2]  Peter G Wolynes,et al.  Protein topology determines binding mechanism. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[3]  Jennifer J. Kohler,et al.  Kinetic studies of Fos.Jun.DNA complex formation: DNA binding prior to dimerization. , 2001, Biochemistry.

[4]  G. Papoian,et al.  Electrostatic, steric, and hydration interactions favor Na(+) condensation around DNA compared with K(+). , 2006, Journal of the American Chemical Society.

[5]  P. Wolynes,et al.  The physics and bioinformatics of binding and folding—an energy landscape perspective , 2003, Biopolymers.

[6]  J. Onuchic,et al.  Theory of Protein Folding This Review Comes from a Themed Issue on Folding and Binding Edited Basic Concepts Perfect Funnel Landscapes and Common Features of Folding Mechanisms , 2022 .

[7]  D Thirumalai,et al.  Effect of finite size on cooperativity and rates of protein folding. , 2006, The journal of physical chemistry. A.

[8]  Tamar Schlick,et al.  Molecular Modeling and Simulation: An Interdisciplinary Guide , 2010 .

[9]  D. Thirumalai,et al.  Mechanical unfolding of RNA hairpins. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[10]  A. Schepartz,et al.  Certain bZIP peptides bind DMA sequentially as monomers and dimerize on the DMA , 1997, Nature Structural Biology.

[11]  S. Takada,et al.  Roles of native topology and chain-length scaling in protein folding: a simulation study with a Go-like model. , 2001, Journal of molecular biology.

[12]  Benjamin A. Shoemaker,et al.  Speeding molecular recognition by using the folding funnel: the fly-casting mechanism. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[13]  Jin Wang,et al.  Single-Molecule Dynamics Reveals Cooperative Binding-Folding in Protein Recognition , 2006, PLoS Comput. Biol..

[14]  J. Marko,et al.  How do site-specific DNA-binding proteins find their targets? , 2004, Nucleic acids research.

[15]  R. Swendsen,et al.  THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method , 1992 .

[16]  Robin S. Dothager,et al.  Random-coil behavior and the dimensions of chemically unfolded proteins. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[17]  Peter G Wolynes,et al.  A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes. , 2005, Journal of molecular biology.

[18]  T Schlick,et al.  Computational modeling predicts the structure and dynamics of chromatin fiber. , 2001, Structure.

[19]  S. Lowen.  The Biophysical Journal , 1960, Nature.

[20]  Peter G Wolynes,et al.  Fly-casting in protein-DNA binding: frustration between protein folding and electrostatics facilitates target recognition. , 2007, Journal of the American Chemical Society.

[21]  S. Takada,et al.  Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms , 2008, Proceedings of the National Academy of Sciences.

[22]  Qiang Lu,et al.  Exploring the mechanism of flexible biomolecular recognition with single molecule dynamics. , 2007, Physical review letters.

[23]  R. Sauer,et al.  Equilibrium dissociation and unfolding of the Arc repressor dimer. , 1989, Biochemistry.

[24]  Robert T. Sauer,et al.  Acceleration of the refolding of Arc repressor by nucleic acids and other polyanions , 1999, Nature Structural Biology.

[25]  C. Wolberger,et al.  Multiprotein-DNA complexes in transcriptional regulation. , 1999, Annual review of biophysics and biomolecular structure.

[26]  C. McMurray,et al.  cAMP Response Element-binding Protein Monomers Cooperatively Assemble to Form Dimers on DNA* , 1998, The Journal of Biological Chemistry.

[27]  M. Ptashne,et al.  Transcriptional activation by recruitment , 1997, Nature.

[28]  M. Zacharias,et al.  Folding of a DNA hairpin loop structure in explicit solvent using replica-exchange molecular dynamics simulations. , 2007, Biophysical journal.

[29]  J. Onuchic,et al.  Theory of protein folding: the energy landscape perspective. , 1997, Annual review of physical chemistry.

[30]  A Libchaber,et al.  Sequence dependent rigidity of single stranded DNA. , 2000, Physical review letters.

[31]  S. McKnight,et al.  Diversity and specificity in transcriptional regulation: the benefits of heterotypic dimerization. , 1991, Trends in biochemical sciences.

[32]  J. Chin,et al.  Gene regulation: Protein escorts to the transcription ball , 1999, Current Biology.

[33]  G. Papoian,et al.  Inter-DNA electrostatics from explicit solvent molecular dynamics simulations. , 2007, Journal of the American Chemical Society.

[34]  S. Acharya,et al.  Single-stranded adenine-rich DNA and RNA retain structural characteristics of their respective double-stranded conformations and show directional differences in stacking pattern. , 2004, Biochemistry.

[35]  G. Rose,et al.  Reassessing random-coil statistics in unfolded proteins. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[36]  J. Liphardt,et al.  Reversible Unfolding of Single RNA Molecules by Mechanical Force , 2001, Science.

[37]  John Kuriyan,et al.  The origin of protein interactions and allostery in colocalization , 2007, Nature.

[38]  Yaakov Levy,et al.  Protein sliding along DNA: dynamics and structural characterization. , 2009, Journal of molecular biology.

[39]  A. Schepartz,et al.  DNA specificity enhanced by sequential binding of protein monomers. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[40]  C L Brooks,et al.  Exploring the origins of topological frustration: design of a minimally frustrated model of fragment B of protein A. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[41]  A. Schepartz,et al.  Effects of nucleic acids and polyanions on dimer formation and DNA binding by bZIP and bHLHZip transcription factors. , 2001, Bioorganic & medicinal chemistry.

[42]  J. Matthews,et al.  The power of two: protein dimerization in biology. , 2004, Trends in biochemical sciences.

[43]  J. Onuchic,et al.  Mechanisms of protein assembly: lessons from minimalist models. , 2006, Accounts of chemical research.

[44]  C. Berger,et al.  Diffusion‐controlled DNA recognition by an unfolded, monomeric bZIP transcription factor , 1998, FEBS letters.

[45]  J. Onuchic,et al.  Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins. , 2000, Journal of molecular biology.

[46]  Robert T. Sauer,et al.  DNA recognition by β-sheets in the Arc represser–operator crystal structure , 1994, Nature.

[47]  Lidia Prieto,et al.  Thermodynamics of Go-type models for protein folding. , 2005, The Journal of chemical physics.

[48]  C. Brooks,et al.  From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding. , 2001, Annual review of physical chemistry.

[49]  T Schlick,et al.  Modeling salt-mediated electrostatics of macromolecules: the discrete surface charge optimization algorithm and its application to the nucleosome. , 2001, Biopolymers.

[50]  A. Baici,et al.  Monomeric and dimeric bZIP transcription factor GCN4 bind at the same rate to their target DNA site. , 2004, Biochemistry.

[51]  Erkang Wang,et al.  Dominant kinetic paths on biomolecular binding-folding energy landscape. , 2006, Physical review letters.

[52]  R. Kaptein,et al.  Nuclear magnetic resonance solution structure of the Arc repressor using relaxation matrix calculations. , 1994, Journal of molecular biology.

[53]  T. Ellenberger,et al.  DNA-mediated Folding and Assembly of MyoD-E47 Heterodimers* , 1998, The Journal of Biological Chemistry.

[54]  Gerhard Hummer,et al.  This is an open-access article distributed under the terms of the Creative Commons Public Domain declara... , 2008 .

[55]  J. Onuchic,et al.  How native-state topology affects the folding of dihydrofolate reductase and interleukin-1beta. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[56]  K. Bjornson,et al.  Kinetic mechanism of DNA binding and DNA-induced dimerization of the Escherichia coli Rep helicase. , 1996, Biochemistry.

[57]  T Schlick,et al.  The influence of salt on the structure and energetics of supercoiled DNA. , 1994, Biophysical journal.

[58]  Nicolas E. Buchler,et al.  On schemes of combinatorial transcription logic , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[59]  S. Pongor,et al.  DNA-mediated assembly of weakly interacting DNA-binding protein subunits: in vitro recruitment of phage 434 repressor and yeast GCN4 DNA-binding domains. , 2004, Nucleic acids research.