Thermodynamics of DNA Binding and Distortion by the Hyperthermophile Chromatin Protein Sac7d

Peters, William B.; Edmondson, Stephen P.; Shriver, John W.

doi:10.1016/j.jmb.2004.08.042

Cited by 40 publications

(57 citation statements)

References 110 publications

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“…Fluorescence titrations and gel shift assays have shown that the affinity of the Sul7d proteins for double-stranded DNA is in the micromolar range in low salt [35,37,38]. However, different estimates of the binding size (36.6 base pairs) were obtained in these studies [35,37,38]. Sul7d is capable of constraining negative DNA supercoils [39,40].…”

Section: Sul7dmentioning

confidence: 99%

Archaeal chromatin proteins

Zhang

Guo

Huang

2012

Sci. China Life Sci.

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Archaea, along with Bacteria and Eukarya, are the three domains of life. In all living cells, chromatin proteins serve a crucial role in maintaining the integrity of the structure and function of the genome. An array of small, abundant and basic DNA-binding proteins, considered candidates for chromatin proteins, has been isolated from the Euryarchaeota and the Crenarchaeota, the two major phyla in Archaea. While most euryarchaea encode proteins resembling eukaryotic histones, crenarchaea appear to synthesize a number of unique DNA-binding proteins likely involved in chromosomal organization. Several of these proteins (e.g., archaeal histones, Sac10b homologs, Sul7d, Cren7, CC1, etc.) have been extensively studied. However, whether they are chromatin proteins and how they function in vivo remain to be fully understood. Future investigation of archaeal chromatin proteins will lead to a better understanding of chromosomal organization and gene expression in Archaea and provide valuable information on the evolution of DNA packaging in cellular life.Archaea, chromatin protein, biochemical properties, structure, post-translational modification Citation:

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Section: Sul7dmentioning

confidence: 99%

Archaeal chromatin proteins

Zhang

Guo

Huang

2012

Sci. China Life Sci.

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“…[2][3][4][5][6][15][16][17][18][19][20][21][22][23][24][25][26][27][28][29][30] For the present analysis, we have selected data obtained under similar conditions (20°C, near neutral pH, 100 mM NaCl) and analyzed by the same approach, namely correcting for refolding effects and resolving the electrostatic and non-electrostatic components of the binding characteristics, as outlined in Figures 1 and 2. All these data are illustrated in Figure 3 and summarized in Table 1 in Supplementary Materials.…”

Section: Thermodynamic Parameters Of Protein-dna Interactionsmentioning

confidence: 99%

What Drives Proteins into the Major or Minor Grooves of DNA?

Privalov

Dragan

Crane‐Robinson

et al. 2007

Journal of Molecular Biology

168

158

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The energetic profiles of a significant number of protein-DNA systems at 20°C reveal that, despite comparable Gibbs free energies, association with the major groove is primarily an enthalpy driven process, whereas binding to the minor groove is characterized by an unfavorable enthalpy that is compensated by favorable entropic contributions. These distinct energetic signatures for major versus minor groove binding are irrespective of the magnitude of DNA bending and/or the extent of binding-induced protein refolding. The primary determinants of their different energetic profiles appear to be the distinct hydration properties of the major and minor grooves, namely that the water in the AT-rich minor groove is in a highly ordered state and its removal results in a substantial positive contribution to the binding entropy. Since the entropic forces driving protein binding into the minor groove are a consequence of displacing water ordered by the regular arrangement of polar contacts, they cannot be regarded as hydrophobic. KeywordsDNA binding; DNA grooves; hydration; thermodynamics; electrostatics Structural and energetic characterizations of protein-nucleic acid complexes are important for a better understanding of the molecular interactions that govern transcriptional regulation. Of particular importance are the energetic profiles of DNA binding domains (DBDs) interacting with their target recognition sites. DBDs are known to interact specifically with either the major or minor grooves of DNA, with binding-induced structural effects ranging from negligible perturbation of the B-DNA conformation to substantial distortions, such as bending and kinking. One can then ask if there are qualitative differences in the forces driving protein binding to the different grooves of DNA. Comparing the association constants of these two types of DBDs does not furnish a satisfactory answer, since both categories contain examples of stronger and weaker binding interactions. An answer to this question therefore requires a detailed analysis of the forces involved in the formation of the specific protein-DNA complexes. This assumes not only measurement of the association constant but also determination of the Gibbs energy and its enthalpic and entropic components over a broad range of conditions, particularly temperature and ionic strength. In this review, we analyze the thermodynamic characteristics of protein binding to DNA published over the last several years. This overall consideration has revealed qualitative differences in the energetic signatures of

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“…(1)-net burial of nonpolar surfaces upon complexation (hydrophobic effect) (18,(20)(21)(22), (2) -changes in the vibrational modes of the macromolecules and participating water (18,23,26), and (3)-thermodynamic coupling of one or more binding or conformational equilibria to the main binding reaction of interest (16)(17)(18)(19)27,28).…”

Section: Nih-pa Author Manuscriptmentioning

confidence: 99%

“…SSB binding to ssDNA is accompanied by a large and negative ΔH obs (as large as ∼ -150 kcal/mol for binding to (dT) 70 at < 10 mM monovalent salt concentration) as well as a large and negative ΔC p,obs (16,17). The molecular basis for a negative ΔC p,obs in macromolecular interactions has been the subject of much interest and discussion (16-26) and several origins have been proposed:(1)-net burial of nonpolar surfaces upon complexation (hydrophobic effect) (18,(20)(21)(22), (2) -changes in the vibrational modes of the macromolecules and participating water (18,23,26), and (3)-thermodynamic coupling of one or more binding or conformational equilibria to the main binding reaction of interest (16)(17)(18)(19)27,28).Our studies of E. coli SSB binding to ssDNA have shown that temperature dependent coupled equilibria contribute significantly to the observed ΔH obs as well as ΔC p,obs . For example, the ΔC p,obs for SSB binding to oligodeoxyadenylates ((dA) N ) is approximately two-fold larger in magnitude than for binding to oligodeoxycytidylates ((dC) N ) or oligodeoxythymidylates ((dT) N ) (16).…”

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confidence: 99%

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Effects of Monovalent Anions on a Temperature-Dependent Heat Capacity Change for Escherichia coli SSB Tetramer Binding to Single-Stranded DNA

Козлов

Lohman

2006

Biochemistry

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We have previously shown that the linkage of temperature-dependent protonation and DNA base unstacking equilibria contribute significantly to both the negative enthalpy change (ΔH obs ) and the negative heat capacity change (ΔC p,obs ) for E. coli SSB homotetramer binding to single stranded (ss) DNA. Using isothermal titration calorimetry we have now examined ΔH obs over a much wider temperature range (5°C to 60°C) and as a function of monovalent salt concentration and type for SSB binding to (dT) 70 under solution conditions that favor the fully wrapped (SSB) 65 complex (monovalent salt concentration ≥ 0.20 M). Over this wider temperature range we observe a strongly temperature dependent ΔC p,obs . The ΔH obs decreases as temperature increases from 5°C to 35°C (ΔC p,obs <0), but then increase at higher temperatures up to 60°C (ΔC p,obs >0). Both salt concentration and anion type have large effects on ΔH obs and ΔC p,obs . These observations can be explained by a model in which SSB protein can undergo a temperature and salt dependent conformational transition (below 35°C), the midpoint of which shifts to higher temperature (above 35°C) for SSB bound to ssDNA. Anions bind weakly to free SSB, with the preference, Br -> Cl -> F -, and these anions are then released upon binding ssDNA, affecting both ΔH obs and ΔC p,obs . We conclude that the experimentally measured values of ΔC p,obs for SSB binding to ssDNA cannot be explained solely on the basis of changes in accessible surface area (ASA) upon complex formation, but rather result from a series of temperature dependent equilibria (ion binding, protonation and protein conformational changes) that are coupled to the SSB-ssDNA binding equilibrium. This is also likely true for many other protein-nucleic acid interactions.Obtaining an understanding of the molecular origins for stability and specificity of proteinnucleic acid interactions is a complex problem. Such interactions not only involve multiple networks of hydrogen bonds, salt bridges and non-polar interactions, but are also accompanied by the coupled binding and/or release of small molecules, such as protons, salt ions and water. These coupled binding equilibria will generally contribute significantly to the thermodynamics of protein-nucleic acid binding (ΔG°, ΔH° and ΔS°). For this reason, thermodynamic information obtained under only one set of solution conditions is generally of limited utility for understanding the origins of stability and specificity of any macromolecular interaction, including protein-nucleic acid binding. † This research was supported in part by the NIH (R01 GM30498) NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author ManuscriptWe have been studying the thermodynamics of E. coli SSB protein binding to single stranded (ss) nucleic acids (for reviews see (1-3)), a protein that is involved in DNA replication, recombination and repair (4). E.coli SSB protein is a stable homotetramer (4×18,843 Da) (5), that can interact with ssDNA in multiple binding modes, depending on...

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Thermodynamics of DNA Binding and Distortion by the Hyperthermophile Chromatin Protein Sac7d

Cited by 40 publications

References 110 publications

Archaeal chromatin proteins

Archaeal chromatin proteins

What Drives Proteins into the Major or Minor Grooves of DNA?

Effects of Monovalent Anions on a Temperature-Dependent Heat Capacity Change for Escherichia coli SSB Tetramer Binding to Single-Stranded DNA

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