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Affinity, Specificity, and Cooperativity of DNA Binding by Bacterial Gene Regulatory Proteins. Int J Mol Sci 2022; 23:ijms23010562. [PMID: 35008987 PMCID: PMC8745587 DOI: 10.3390/ijms23010562] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/14/2021] [Accepted: 12/22/2021] [Indexed: 12/04/2022] Open
Abstract
Nearly all of biology depends on interactions between molecules: proteins with small molecules, proteins with other proteins, nucleic acids with small molecules, and nucleic acids with proteins that regulate gene expression, our concern in this Special Issue. All those kinds of interactions, and others, constitute the vast majority of biology at the molecular level. An understanding of those interactions requires that we quantify them to learn how they interact: How strongly? With which partners? How—and how well—are different partners distinguished? This review addresses the evolution of our current understanding of the molecular origins of affinity and specificity in regulatory protein–DNA interactions, and suggests that both these properties can be modulated by cooperativity.
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Pandey SK, Melichercik M, Řeha D, Ettrich RH, Carey J. Conserved Dynamic Mechanism of Allosteric Response to L-arg in Divergent Bacterial Arginine Repressors. Molecules 2020; 25:molecules25092247. [PMID: 32397647 PMCID: PMC7248756 DOI: 10.3390/molecules25092247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/08/2020] [Accepted: 05/09/2020] [Indexed: 11/23/2022] Open
Abstract
Hexameric arginine repressor, ArgR, is the feedback regulator of bacterial L-arginine regulons, and sensor of L-arg that controls transcription of genes for its synthesis and catabolism. Although ArgR function, as well as its secondary, tertiary, and quaternary structures, is essentially the same in E. coli and B. subtilis, the two proteins differ significantly in sequence, including residues implicated in the response to L-arg. Molecular dynamics simulations are used here to evaluate the behavior of intact B. subtilis ArgR with and without L-arg, and are compared with prior MD results for a domain fragment of E. coli ArgR. Relative to its crystal structure, B. subtilis ArgR in absence of L-arg undergoes a large-scale rotational shift of its trimeric subassemblies that is very similar to that observed in the E. coli protein, but the residues driving rotation have distinct secondary and tertiary structural locations, and a key residue that drives rotation in E. coli is missing in B. subtilis. The similarity of trimer rotation despite different driving residues suggests that a rotational shift between trimers is integral to ArgR function. This conclusion is supported by phylogenetic analysis of distant ArgR homologs reported here that indicates at least three major groups characterized by distinct sequence motifs but predicted to undergo a common rotational transition. The dynamic consequences of L-arg binding for transcriptional activation of intact ArgR are evaluated here for the first time in two-microsecond simulations of B. subtilis ArgR. L-arg binding to intact B. subtilis ArgR causes a significant further shift in the angle of rotation between trimers that causes the N-terminal DNA-binding domains lose their interactions with the C-terminal domains, and is likely the first step toward adopting DNA-binding-competent conformations. The results aid interpretation of crystal structures of ArgR and ArgR-DNA complexes.
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Affiliation(s)
- Saurabh Kumar Pandey
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Czech Academy of Sciences, 37333 Nove Hrady, Czechia; (S.K.P.); (M.M.); (D.Ř.)
- Department of Nuclear Physics and Biophysics, Faculty of Mathematics, Physics, and Informatics, Comenius University in Bratislava, 84248 Bratislava, Slovakia
- Faculty of Sciences, University of South Bohemia, 37005 Ceske Budejovice, Czechia
| | - Milan Melichercik
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Czech Academy of Sciences, 37333 Nove Hrady, Czechia; (S.K.P.); (M.M.); (D.Ř.)
- Department of Nuclear Physics and Biophysics, Faculty of Mathematics, Physics, and Informatics, Comenius University in Bratislava, 84248 Bratislava, Slovakia
| | - David Řeha
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Czech Academy of Sciences, 37333 Nove Hrady, Czechia; (S.K.P.); (M.M.); (D.Ř.)
- Faculty of Sciences, University of South Bohemia, 37005 Ceske Budejovice, Czechia
| | - Rüdiger H. Ettrich
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Czech Academy of Sciences, 37333 Nove Hrady, Czechia; (S.K.P.); (M.M.); (D.Ř.)
- College of Biomedical Sciences, Larkin University, Miami, FL 33169, USA
- Department of Cellular Biology & Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
- Correspondence: (R.H.E.); (J.C.); Tel.: +1-954-682-8347 (R.H.E.); +1-609-258-1631 (J.C.)
| | - Jannette Carey
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Czech Academy of Sciences, 37333 Nove Hrady, Czechia; (S.K.P.); (M.M.); (D.Ř.)
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
- Correspondence: (R.H.E.); (J.C.); Tel.: +1-954-682-8347 (R.H.E.); +1-609-258-1631 (J.C.)
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Carey J, Benoff B, Harish B, Yuan L, Lawson CL. Environment-dependent long-range structural distortion in a temperature-sensitive point mutant. Protein Sci 2012; 21:63-74. [PMID: 22057811 PMCID: PMC3323781 DOI: 10.1002/pro.759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Revised: 10/25/2011] [Accepted: 10/27/2011] [Indexed: 01/07/2023]
Abstract
Extensive environment-dependent rearrangement of the helix-turn-helix DNA recognition region and adjacent L-tryptophan binding pocket is reported in the crystal structure of dimeric E. coli trp aporepressor with point mutation Leu75Phe. In one of two subunits, the eight residues immediately C-terminal to the mutation are shifted forward in helical register by three positions, and the five following residues form an extrahelical loop accommodating the register shift. In contrast, the second subunit has wildtype-like conformation, as do both subunits in an isomorphous wildtype control structure. Treated together as an ensemble pair, the distorted and wildtype-like conformations of the mutant apoprotein agree more fully than either conformation alone with previously reported NOE measurements, and account more completely for its diverse biochemical and biophysical properties. The register-shifted segment Ile79-Ala80-Thr81-Ile82-Thr83 is helical in both conformations despite low helical propensity, suggesting an important structural role for the steric constraints imposed by β-branched residues in helical conformation.
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Affiliation(s)
- Jannette Carey
- Chemistry Department, Princeton UniversityPrinceton, New Jersey 08544,*Correspondence to: Jannette Carey, Chemistry Department, Princeton University, Princeton, NJ 08544. E-mail: or Catherine L. Lawson, Department of Chemistry & Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854. E-mail:
| | - Brian Benoff
- Department of Chemistry & Chemical Biology, Rutgers, The State University of New JerseyPiscataway New Jersey 08854
| | | | - Lara Yuan
- Chemistry Department, Princeton UniversityPrinceton, New Jersey 08544
| | - Catherine L Lawson
- Department of Chemistry & Chemical Biology, Rutgers, The State University of New JerseyPiscataway New Jersey 08854,*Correspondence to: Jannette Carey, Chemistry Department, Princeton University, Princeton, NJ 08544. E-mail: or Catherine L. Lawson, Department of Chemistry & Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854. E-mail:
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Strawn R, Melichercik M, Green M, Stockner T, Carey J, Ettrich R. Symmetric allosteric mechanism of hexameric Escherichia coli arginine repressor exploits competition between L-arginine ligands and resident arginine residues. PLoS Comput Biol 2010; 6:e1000801. [PMID: 20532206 PMCID: PMC2880562 DOI: 10.1371/journal.pcbi.1000801] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Accepted: 04/29/2010] [Indexed: 12/20/2022] Open
Abstract
An elegantly simple and probably ancient molecular mechanism of allostery is described for the Escherichia coli arginine repressor ArgR, the master feedback regulator of transcription in L-arginine metabolism. Molecular dynamics simulations with ArgRC, the hexameric domain that binds L-arginine with negative cooperativity, reveal that conserved arginine and aspartate residues in each ligand-binding pocket promote rotational oscillation of apoArgRC trimers by engagement and release of hydrogen-bonded salt bridges. Binding of exogenous L-arginine displaces resident arginine residues and arrests oscillation, shifting the equilibrium quaternary ensemble and promoting motions that maintain the configurational entropy of the system. A single L-arg ligand is necessary and sufficient to arrest oscillation, and enables formation of a cooperative hydrogen-bond network at the subunit interface. The results are used to construct a free-energy reaction coordinate that accounts for the negative cooperativity and distinctive thermodynamic signature of L-arginine binding detected by calorimetry. The symmetry of the hexamer is maintained as each ligand binds, despite the conceptual asymmetry of partially-liganded states. The results thus offer the first opportunity to describe in structural and thermodynamic terms the symmetric relaxed state predicted by the concerted allostery model of Monod, Wyman, and Changeux, revealing that this state is achieved by exploiting the dynamics of the assembly and the distributed nature of its cohesive free energy. The ArgR example reveals that symmetry can be maintained even when binding sites fill sequentially due to negative cooperativity, which was not anticipated by the Monod, Wyman, and Changeux model. The molecular mechanism identified here neither specifies nor requires a pathway for transmission of the allosteric signal through the protein, and it suggests the possibility that binding of free amino acids was an early innovation in the evolution of allostery.
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Affiliation(s)
- Rebecca Strawn
- Chemistry Department, Princeton University, Princeton, New Jersey, United States of America
| | - Milan Melichercik
- Department of Structure and Function of Proteins, Institute of Systems Biology and Ecology, Academy of Sciences of the Czech Republic, and Institute of Physical Biology, University of South Bohemia, Nove Hrady, Czech Republic
| | - Michael Green
- Biology Department, The College of New Jersey, Ewing, New Jersey, United States of America
| | - Thomas Stockner
- Department of Medical Chemistry, Medical University of Vienna, Vienna, Austria
| | - Jannette Carey
- Chemistry Department, Princeton University, Princeton, New Jersey, United States of America
| | - Rüdiger Ettrich
- Department of Structure and Function of Proteins, Institute of Systems Biology and Ecology, Academy of Sciences of the Czech Republic, and Institute of Physical Biology, University of South Bohemia, Nove Hrady, Czech Republic
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Carey J, Lindman S, Bauer M, Linse S. Protein reconstitution and three-dimensional domain swapping: benefits and constraints of covalency. Protein Sci 2007; 16:2317-33. [PMID: 17962398 PMCID: PMC2211703 DOI: 10.1110/ps.072985007] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2007] [Revised: 07/30/2007] [Accepted: 08/01/2007] [Indexed: 10/22/2022]
Abstract
The phenomena of protein reconstitution and three-dimensional domain swapping reveal that highly similar structures can be obtained whether a protein is comprised of one or more polypeptide chains. In this review, we use protein reconstitution as a lens through which to examine the range of protein tolerance to chain interruptions and the roles of the primary structure in related features of protein structure and folding, including circular permutation, natively unfolded proteins, allostery, and amyloid fibril formation. The results imply that noncovalent interactions in a protein are sufficient to specify its structure under the constraints imposed by the covalent backbone.
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Affiliation(s)
- Jannette Carey
- Chemistry Department, Princeton University, NJ 08544-1009, USA.
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Danelon C, Suenaga A, Winterhalter M, Yamato I. Molecular origin of the cation selectivity in OmpF porin: single channel conductances vs. free energy calculation. Biophys Chem 2003; 104:591-603. [PMID: 12914905 DOI: 10.1016/s0301-4622(03)00062-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Ion current through single outer membrane protein F (OmpF) trimers was recorded and compared to molecular dynamics simulation. Unidirectional insertion was revealed from the asymmetry in channel conductance. Single trimer conductance showed particularly high values at low symmetrical salt solution. The conductance values of various alkali metal ion solutions were proportional to the monovalent cation mobility values in the bulk phase, LiCl<NaCl<KCl<RbCl approximately CsCl, but the conductance differences were quantitatively larger than conductivity differences in bulk solutions. Selectivity measurements at low concentration showed that OmpF channels favored permeation of alkali metal ions over chloride and suggested size preference for smaller cations. These results suggest that there are specific interactions between the permeating cation and charged residues lining the channel walls. This hypothesis was supported by computational study which predicted that monovalent cations bind to Asp113 at low concentration. Here, free energy calculations revealed that the affinity of the alkali metal ions to its binding site increased with their atomic radii, Li(+) approximately Na(+)<K(+) approximately Rb(+) approximately Cs(+). A detailed inspection of both experimental and computational results suggested that stronger binding at the central constriction of the channel increases the translocation rate of cations under applied voltage by increasing their local concentration relative to the bulk solution.
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Affiliation(s)
- Christophe Danelon
- Institut de Pharmacologie et de Biologie Structurale, CNRS-UMR 5089, Universite P. Sabatier, 205 route de Narbonne, 31077 Toulouse, France
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Suenaga A, Yatsu C, Komeiji Y, Uebayasi M, Meguro T, Yamato I. Molecular dynamics simulation of trp-repressor/operator complex: analysis of hydrogen bond patterns of protein–DNA interaction. J Mol Struct 2000. [DOI: 10.1016/s0022-2860(00)00459-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Tomic S, Nilsson L, Wade RC. Nuclear receptor-DNA binding specificity: A COMBINE and Free-Wilson QSAR analysis. J Med Chem 2000; 43:1780-92. [PMID: 10794695 DOI: 10.1021/jm9911175] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Specific binding of transcription factors to DNA is crucial for gene regulation. We derived models for the binding specificity of transcription factors of the nuclear receptor family to DNA using two QSAR methods: a Free-Wilson-like method and COMparative BINding Energy (COMBINE) analysis. The analysis is based on experimental data for the interaction of 20 mutant glucocorticoid receptor DNA-binding domains with 16 different response elements in a total of 320 complexes (Zilliacus, J.; Wright, A. P.; Carlstedt-Duke, J.; Nilsson, L.; Gustafsson, J. A. Proteins 1995, 21, 57-67). The predictive abilities of the models obtained by the two methods are similar. The COMBINE analysis indicates that the most important properties for determining binding specificity for this dataset are the changes upon binding of the solvation free energies of the bases that are mutated in the dataset and the electrostatic interactions of the mutated nucleotides with certain charged amino acids. Further important descriptors are the changes of solvation free energy and surface area of the side chain of the mutated residue. It is clear, however, that there are additional features important for the specificity of binding that are not included in the models, such as differences in interfacial hydration of the complexes.
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Affiliation(s)
- S Tomic
- European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
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Abstract
The wild-type trp repressor of E. coli bound 5-methoxytryptophan, a Trp analogue, less tightly than Trp. A mutant repressor (Val58-->Ala) that should bind 5-methoxytryptophan preferentially to Trp was computationally designed by free-energy calculations accompanied by free-energy decomposition. The designed mutant was demonstrated by experiments to bind 5-methoxytryptophan more tightly than Trp, consistent with the computational prediction. This success indicates the usefulness of free energy decomposition in protein design.
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Affiliation(s)
- N Honda
- Department of Biological Science and Technology, Science University of Tokyo, Chiba, Japan
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