101
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Baranovskii SF, Chernyshev DN, Buchel’nikov AS, Evstigneev MP. Thermodynamic analysis of complex formation of ethidium bromide with DNA in water solutions. Biophysics (Nagoya-shi) 2011. [DOI: 10.1134/s0006350911020023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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102
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Human U2B″ protein binding to snRNA stemloops. Biophys Chem 2011; 159:82-9. [PMID: 21684671 DOI: 10.1016/j.bpc.2011.05.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2011] [Revised: 05/09/2011] [Accepted: 05/09/2011] [Indexed: 11/24/2022]
Abstract
The human U2B″ protein is one of the unique proteins that comprise the U2 snRNP, but it is also a representative of the U1A/U2B″ protein family. In the U2 snRNP, it is bound to Stem-Loop IV (SLIV) of the U2 snRNA. We find that in vitro it binds not only to human SLIV, but also to Stem-Loop II (SLII) from human U1 snRNA and to Drosophila U2 snRNA SLIV. The thermodynamics of these binding interactions show a striking similarity, leading to the conclusion that U2B″ has a relaxed specificity for its RNA targets. The binding properties of U2B″ are distinct from those of human U1A and of Drosophila SNF, despite its high homology to those proteins, and so provide important new information on how this protein family has modulated its target preferences.
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103
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Kozlov AG, Lohman TM. E. coli SSB tetramer binds the first and second molecules of (dT)(35) with heat capacities of opposite sign. Biophys Chem 2011; 159:48-57. [PMID: 21636209 DOI: 10.1016/j.bpc.2011.05.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Revised: 05/02/2011] [Accepted: 05/02/2011] [Indexed: 11/17/2022]
Abstract
We have previously shown that formation of a 1:1 fully wrapped complex of Escherichia coli SSB tetramer with (dT)(70) displays a temperature-dependent sign reversal of the binding heat capacity (ΔC(P)). Here we examine SSB binding to shorter oligodeoxynucleotides ((dX)(35)) to probe whether this effect requires binding of one or two (dX)(35) molecules per SSB tetramer. We find that the ΔC(P) for the first molecule of (dX)(35) is always negative. However, a sign reversal of ΔC(P) from negative to positive occurs with increasing temperature for binding of the second (dX)(35). This striking behavior of ΔC(P) for the second (dX)(35) appears linked to conformational changes within the ssDNA-SSB complex that are required to form a fully wrapped (SSB)(65) binding mode. These results also underscore that binding heat capacities of macromolecular interactions have multiple origins that cannot be understood simply on the basis of examining static structures.
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Affiliation(s)
- Alexander G Kozlov
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, United States
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104
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Interaction of berberine, palmatine, coralyne, and sanguinarine to quadruplex DNA: A comparative spectroscopic and calorimetric study. Biochim Biophys Acta Gen Subj 2011; 1810:485-96. [DOI: 10.1016/j.bbagen.2011.01.011] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Revised: 01/21/2011] [Accepted: 01/24/2011] [Indexed: 12/11/2022]
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105
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Bhattacharjee N, Biswas P. Position-specific propensities of amino acids in the β-strand. BMC STRUCTURAL BIOLOGY 2010; 10:29. [PMID: 20920153 PMCID: PMC2955036 DOI: 10.1186/1472-6807-10-29] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Accepted: 09/28/2010] [Indexed: 11/23/2022]
Abstract
Background Despite the importance of β-strands as main building blocks in proteins, the propensity of amino acid in β-strands is not well-understood as it has been more difficult to determine experimentally compared to α-helices. Recent studies have shown that most of the amino acids have significantly high or low propensity towards both ends of β-strands. However, a comprehensive analysis of the sequence dependent amino acid propensities at positions between the ends of the β-strand has not been investigated. Results The propensities of the amino acids calculated from a large non-redundant database of proteins are found to be highly position-specific and vary continuously throughout the length of the β-strand. They follow an unexpected characteristic periodic pattern in inner positions with respect to the cap residues in both termini of β-strands; this periodic nature is markedly different from that of the α-helices with respect to the strength and pattern in periodicity. This periodicity is not only different for different amino acids but it also varies considerably for the amino acids belonging to the same physico-chemical group. Average hydrophobicity is also found to be periodic with respect to the positions from both termini of β-strands. Conclusions The results contradict the earlier perception of isotropic nature of amino acid propensities in the middle region of β-strands. These position-specific propensities should be of immense help in understanding the factors responsible for β-strand design and efficient prediction of β-strand structure in unknown proteins.
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106
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Fisicaro E, Compari C, Braibanti A. Hydrophobic hydration processes. General thermodynamic model by thermal equivalent dilution determinations. Biophys Chem 2010; 151:119-38. [PMID: 20656401 DOI: 10.1016/j.bpc.2010.06.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Revised: 06/10/2010] [Accepted: 06/10/2010] [Indexed: 10/19/2022]
Abstract
The "hydrophobic hydration processes" can be satisfactorily interpreted on the basis of a common molecular model for water, consisting of two types of clusters, namely W(I) and W(II) accompanied by free molecules W(III). The principle of thermal equivalent dilution (TED) is the potent tool (Ergodic Hypothesis) employed to monitor the water equilibrium and to determine the number xi(w) of water molecules W(III) involved in each process. The hydrophobic hydration processes can be subdivided into two Classes: Class A includes those processes for which the transformation A(-xi(w)W(I)-->xi(w)W(II)+xi(w)W(III)+cavity) takes place with the formation of a cavity, by expulsion of xi(w) water molecules W(III) whereas Class B includes those processes for which the opposite transformation B(-xi(w)W(II)-xi(w)W(III)-->xi(w)W(I)-cavity) takes place with reduction of the cavity, by condensation of xi(w) water molecules W(III). The number xi(w) depends on the size of the reactants and measures the extent of the change in volume of the cavity. Disaggregating the thermodynamic functions DeltaH(app) and DeltaS(app) as the functions of T (or lnT) and xi(w) has enabled the separation of the thermodynamic functions into work and thermal components. The work functions DeltaG(Work), DeltaH(Work) and DeltaS(Work) only refer specifically to the hydrophobic effects of cavity formation or cavity reduction, respectively. The constant self-consistent unitary (xi(w)=1) work functions obtained from both large and small molecules indicate that the same unitary reaction is taking place, independent from the reactant size. The thermal functions DeltaH(Th) and DeltaS(Th) refer exclusively to the passage of state of water W(III). Essential mathematical algorithms are presented in the appendices.
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Affiliation(s)
- E Fisicaro
- Dept. of Pharmacological, Biological, and Applied Chemical Sciences, University of Parma, Italy
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107
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Chowdhury SR, Islam MM, Kumar GS. Binding of the anticancer alkaloid sanguinarine to double stranded RNAs: insights into the structural and energetics aspects. MOLECULAR BIOSYSTEMS 2010; 6:1265-76. [PMID: 20442937 DOI: 10.1039/b927001a] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Elucidation of the molecular aspects of small molecule-RNA complexation is of prime importance for rational RNA targeted drug design strategies. Towards this, the interaction of the cytotoxic plant alkaloid sanguinarine to three double stranded ribonucleic acids, poly (A).poly(U), poly(I).poly(C) and poly(C).poly(G) was studied using various biophysical and thermodynamic techniques. Absorbance and fluorescence studies showed that the alkaloid bound cooperatively to these RNAs with binding affinities of the order 10(4) M(-1). Fluorescence quenching and hydrodynamic studies gave evidence for intercalation of sanguinarine to these RNA duplexes. Isothermal titration calorimetric studies revealed that the binding was characterized by negative enthalpy and positive entropy changes and the affinity constants derived were in agreement with the overall binding affinity values obtained from spectroscopic data. The binding of sanguinarine stabilized the melting of poly(A). poly(U) and poly(I).poly(C) and the binding data evaluated from the melting data were in agreement with that obtained from other techniques. The overall binding affinity of sanguinarine to these double stranded RNAs varied in the order, poly(A).poly(U) > poly(I).poly(C) >> poly(C).poly(G). The temperature dependence of the enthalpy changes afforded negative values of heat capacity changes for the binding of sanguinarine to poly(A).poly(U) and poly(I).poly(C), suggesting substantial hydrophobic contribution in the binding process. Further, enthalpy-entropy compensation phenomena was also seen in poly(A).poly(U) and poly(I).poly(C) systems that correlated to the strong binding involving a multiplicity of weak noncovalent interactions compared to the weak binding with poly(C).poly(G). These results further advance our understanding on the binding of small molecules that are specific binders to double stranded RNA sequences.
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Affiliation(s)
- Sebanti Roy Chowdhury
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology (CSIR), 4, Raja S. C. Mullick Road, Kolkata 700032, India
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108
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Paul P, Hossain M, Yadav RC, Kumar GS. Biophysical studies on the base specificity and energetics of the DNA interaction of photoactive dye thionine: Spectroscopic and calorimetric approach. Biophys Chem 2010; 148:93-103. [DOI: 10.1016/j.bpc.2010.02.015] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Revised: 02/22/2010] [Accepted: 02/23/2010] [Indexed: 12/01/2022]
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109
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Xi H, Kumar S, Dosen-Micovic L, Arya DP. Calorimetric and spectroscopic studies of aminoglycoside binding to AT-rich DNA triple helices. Biochimie 2010; 92:514-29. [PMID: 20167243 PMCID: PMC3977217 DOI: 10.1016/j.biochi.2010.02.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2009] [Accepted: 02/08/2010] [Indexed: 11/21/2022]
Abstract
Calorimetric and fluorescence techniques were used to characterize the binding of aminoglycosides-neomycin, paromomycin, and ribostamycin, with 5'-dA(12)-x-dT(12)-x-dT(12)-3' intramolecular DNA triplex (x = hexaethylene glycol) and poly(dA).2poly(dT) triplex. Our results demonstrate the following features: (1) UV thermal analysis reveals that the T(m) for triplex decreases with increasing pH value in the presence of neomycin, while the T(m) for the duplex remains unchanged. (2) The binding affinity of neomycin decreases with increased pH, although there is an increase in observed binding enthalpy. (3) ITC studies conducted in two buffers (sodium cacodylate and MOPS) yield the number of protonated drug amino groups (Deltan) as 0.29 and 0.40 for neomycin and paromomycin interaction with 5'-dA(12)-x-dT(12)-x-dT(12)-3', respectively. (4) The specific heat capacity change (DeltaC(p)) determined by ITC studies is negative, with more negative values at lower salt concentrations. From 100 mM to 250 mM KCl, the DeltaC(p) ranges from -402 to -60 cal/(mol K) for neomycin. At pH 5.5, a more positive DeltaC(p) is observed, with a value of -98 cal/(mol K) at 100 mM KCl. DeltaC(p) is not significantly affected by ionic strength. (5) Salt dependence studies reveal that there are at least three amino groups of neomycin participating in the electrostatic interactions with the triplex. (6) FID studies using thiazole orange were used to derive the AC(50) (aminoglycoside concentration needed to displace 50% of the dye from the triplex) values. Neomycin shows a seven fold higher affinity than paromomycin and eleven fold higher affinity than ribostamycin at pH 6.8. (7) Modeling studies, consistent with UV and ITC results, show the importance of an additional positive charge in triplex recognition by neomycin. The modeling and thermodynamic studies indicate that neomycin binding to the DNA triplex depends upon significant contributions from charge as well as shape complementarity of the drug to the DNA triplex Watson-Hoogsteen groove.
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Affiliation(s)
- Hongjuan Xi
- Contribution from the Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, USA
| | - Sunil Kumar
- Contribution from the Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, USA
| | - Ljiljana Dosen-Micovic
- Contribution from the Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, USA
| | - Dev P. Arya
- Contribution from the Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, USA
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110
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Weiss TC, Zhai GG, Bhatia SS, Romaniuk PJ. An RNA aptamer with high affinity and broad specificity for zinc finger proteins. Biochemistry 2010; 49:2732-40. [PMID: 20175561 DOI: 10.1021/bi9016654] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A class of RNA aptamers that demonstrates a high affinity for a large variety of C(2)H(2) zinc finger proteins was isolated from a library of random RNA sequences by the zinc finger protein TFIIIA. These aptamers have one or more copies of the consensus sequence GGGUGGG, which is part of a putative hairpin loop in the proposed structure of the most abundant aptamer, RNA1. Binding of zinc finger proteins to RNA1 relies upon zinc-dependent folding of the protein, the affinity of an individual protein for RNA1 being determined by the number of tandem zinc finger motifs. The properties of RNA1 were compared to the properties of two other aptamers from the same selection experiment: RNA21, which binds to some but not all zinc finger proteins tested, and RNA22, which binds only to the 5S rRNA binding zinc finger proteins TFIIIA and p43. The binding of three different zinc finger proteins to RNA1 was compared, and the results indicate that the RNA1-protein interaction occurs by several distinct mechanisms. Mutagenesis of RNA1 confirmed that the GGGUGGG consensus sequence presented in a hairpin conformation is required for high-affinity binding of zinc finger proteins.
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Affiliation(s)
- Tristen C Weiss
- Department of Biochemistry and Microbiology, University of Victoria, P.O. Box 3055, Victoria, BC V8W 3P6, Canada
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111
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Ferreiro DU, Komives EA. Molecular mechanisms of system control of NF-kappaB signaling by IkappaBalpha. Biochemistry 2010; 49:1560-7. [PMID: 20055496 DOI: 10.1021/bi901948j] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The NF-kappaB family of transcription factors responds to inflammatory cytokines with rapid transcriptional activation and subsequent signal repression. Much of the system control depends on the unique characteristics of its major inhibitor, IkappaBalpha, which appears to have folding dynamics that underlie the biophysical properties of its activity. Theoretical folding studies followed by experiments have shown that a portion of the ankyrin repeat domain of IkappaBalpha folds on binding. In resting cells, IkappaBalpha is constantly being synthesized, but most of it is rapidly degraded, leaving only a very small pool of free IkappaBalpha. Nearly all of the NF-kappaB is bound to IkappaBalpha, resulting in near-complete inhibition of nuclear localization and transcriptional activation. Combined solution biophysical measurements and quantitative protein half-life measurements inside cells have allowed us to understand how the inhibition occurs, why IkappaBalpha can be degraded quickly in the free state but remain extremely stable in the bound state, and how signal activation and repression can be tuned by IkappaB folding dynamics. This review summarizes results of in vitro and in vivo experiments that converge demonstrating the effective interplay between biophysics and cell biology in understanding transcriptional control by the NF-kappaB signaling module.
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Affiliation(s)
- Diego U Ferreiro
- Laboratorio de Expresion y Plegado de Proteinas, Universidad Nacional de Quilmes, Roque Saenz Pena 352,B1876BXD Bernal, Buenos Aires, Argentina
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112
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Weiss TC, Zhai GG, Romaniuk PJ. An RNA aptamer with high affinity and high specificity for the 5S RNA binding zinc finger proteins TFIIIA and p43. Biochemistry 2010; 49:1755-65. [PMID: 20095591 DOI: 10.1021/bi901664h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Xenopus zinc finger proteins TFIIIA and p43 bind to 5S RNA in immature oocytes to form 7S and 42S ribonucleoprotein storage particles. To probe the similarities and differences in the RNA binding domains of these two proteins, a library of random RNA molecules was enriched using TFIIIA as the bait protein. One of the abundant aptamers isolated, RNA22, bound to both TFIIIA and p43 derived zinc finger peptides with high affinity and specificity even though the predicted secondary structure of the RNA was unrelated to that of 5S RNA. The interactions of TFIIIA and p43 peptides with RNA22 were compared to their interactions with 5S RNA by characterizing the effects of assay conditions, mutations in RNA22, and mutations in the zinc finger proteins. The similarities and differences in the mechanisms by which these two zinc finger proteins interact with 5S RNA compared to RNA22 suggest they share a common platform for RNA binding with enough flexibility to form specific interactions with both RNAs.
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Affiliation(s)
- Tristen C Weiss
- Department of Biochemistry and Microbiology, University of Victoria, P.O. Box 3055, Victoria, British Columbia V8W 3P6, Canada
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113
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Piccinini M, Scandroglio F, Prioni S, Buccinnà B, Loberto N, Aureli M, Chigorno V, Lupino E, DeMarco G, Lomartire A, Rinaudo MT, Sonnino S, Prinetti A. Deregulated sphingolipid metabolism and membrane organization in neurodegenerative disorders. Mol Neurobiol 2010; 41:314-40. [PMID: 20127207 DOI: 10.1007/s12035-009-8096-6] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Accepted: 12/22/2009] [Indexed: 12/13/2022]
Abstract
Sphingolipids are polar membrane lipids present as minor components in eukaryotic cell membranes. Sphingolipids are highly enriched in nervous cells, where they exert important biological functions. They deeply affect the structural and geometrical properties and the lateral order of cellular membranes, modulate the function of several membrane-associated proteins, and give rise to important intra- and extracellular lipid mediators. Sphingolipid metabolism is regulated along the differentiation and development of the nervous system, and the expression of a peculiar spatially and temporarily regulated sphingolipid pattern is essential for the maintenance of the functional integrity of the nervous system: sphingolipids in the nervous system participate to several signaling pathways controlling neuronal survival, migration, and differentiation, responsiveness to trophic factors, synaptic stability and synaptic transmission, and neuron-glia interactions, including the formation and stability of central and peripheral myelin. In several neurodegenerative diseases, sphingolipid metabolism is deeply deregulated, leading to the expression of abnormal sphingolipid patterns and altered membrane organization that participate to several events related to the pathogenesis of these diseases. The most impressive consequence of this deregulation is represented by anomalous sphingolipid-protein interactions that are at least, in part, responsible for the misfolding events that cause the fibrillogenic and amyloidogenic processing of disease-specific protein isoforms, such as amyloid beta peptide in Alzheimer's disease, huntingtin in Huntington's disease, alpha-synuclein in Parkinson's disease, and prions in transmissible encephalopathies. Targeting sphingolipid metabolism represents today an underexploited but realistic opportunity to design novel therapeutic strategies for the intervention in these diseases.
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Affiliation(s)
- Marco Piccinini
- Section of Biochemistry, Department of Medicine and Experimental Oncology, University of Turin, Turin, Italy
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114
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Kostjukov VV, Khomytova NM, Evstigneev MP. Partition of thermodynamic energies of drug-DNA complexation. Biopolymers 2009; 91:773-90. [DOI: 10.1002/bip.21227] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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115
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Hossain M, Suresh Kumar G. DNA intercalation of methylene blue and quinacrine: new insights into base and sequence specificity from structural and thermodynamic studies with polynucleotides. MOLECULAR BIOSYSTEMS 2009; 5:1311-22. [PMID: 19823747 DOI: 10.1039/b909563b] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The binding of the known DNA intercalators methylene blue and quinacrine with four sequence specific polynucleotides, viz. poly(dG-dC).poly(dG-dC), poly(dG).poly(dC), poly(dA-dT).poly(dA-dT) and poly(dA).poly(dT), have been compared using absorbance, fluorescence, competition dialysis and thermal melting and the thermodynamic aspects of the interaction studied. In all the cases, non-cooperative binding phenomena obeying neighbor exclusion principle was observed though the affinity was remarkably higher for quinacrine and the nature of the binding was characterized to be true intercalation. The data on the salt dependence of binding derived from the plot of log Kvs. log[Na(+)] revealed a slope of around 1.0, consistent with the values predicted by the theories for the binding of monovalent cations, and contained contributions from polyelectrolytic and non-polyelectrolytic forces. The bindings were characterized by strong stabilization of the polynucleotides against thermal strand separation in both optical melting as well as differential scanning calorimetry studies. The data analyzed from the thermal melting and isothermal titration calorimetry studies were in close proximity to those obtained from absorption spectral titration data. Isothermal titration calorimetry results revealed the bindings to poly(dG-dC).poly(dG-dC), poly(dG).poly(dC) and poly(dA-dT).poly(dA-dT) to be exothermic and favoured by both negative enthalpy and large favourable positive entropy changes, while that to poly(dA).poly(dT) was endothermic and entropy driven. The heat capacity changes obtained from temperature dependence of enthalpy gave negative values to all polynucleotides. New insights on the molecular aspects of interaction of these molecules to DNA have emerged from these studies.
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Affiliation(s)
- Maidul Hossain
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology (Council of Scientific and Industrial Research), 4, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
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116
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Dorvel B, Sigalov G, Zhao Q, Comer J, Dimitrov V, Mirsaidov U, Aksimentiev A, Timp G. Analyzing the forces binding a restriction endonuclease to DNA using a synthetic nanopore. Nucleic Acids Res 2009; 37:4170-9. [PMID: 19433506 PMCID: PMC2709577 DOI: 10.1093/nar/gkp317] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2008] [Revised: 04/17/2009] [Accepted: 04/19/2009] [Indexed: 11/14/2022] Open
Abstract
Restriction endonucleases are used prevalently in recombinant DNA technology because they bind so stably to a specific target sequence and, in the presence of cofactors, cleave double-helical DNA specifically at a target sequence at a high rate. Using synthetic nanopores along with molecular dynamics (MD), we have analyzed with atomic resolution how a prototypical restriction endonuclease, EcoRI, binds to the DNA target sequence--GAATTC--in the absence of a Mg(2+) ion cofactor. We have previously shown that there is a voltage threshold for permeation of DNA bound to restriction enzymes through a nanopore that is associated with a nanonewton force required to rupture the complex. By introducing mutations in the DNA, we now show that this threshold depends on the recognition sequence and scales linearly with the dissociation energy, independent of the pore geometry. To predict the effect of mutation in a base pair on the free energy of dissociation, MD is used to qualitatively rank the stability of bonds in the EcoRI-DNA complex. We find that the second base in the target sequence exhibits the strongest binding to the protein, followed by the third and first bases, with even the flanking sequence affecting the binding, corroborating our experiments.
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Affiliation(s)
| | | | | | | | | | | | | | - G. Timp
- Beckman Institute, University of Illinois, Urbana, IL 61801, USA
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117
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Islam MM, Chowdhury SR, Kumar GS. Spectroscopic and calorimetric studies on the binding of alkaloids berberine, palmatine and coralyne to double stranded RNA polynucleotides. J Phys Chem B 2009; 113:1210-24. [PMID: 19132839 DOI: 10.1021/jp806597w] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The interaction of two natural protoberberine plant alkaloids berberine and palmatine and a synthetic derivative coralyne to three double stranded ribonucleic acids, poly(A). poly(U), poly(I).poly(C) and poly(C).poly(G) was studied using various biophysical techniques. Absorbance and fluorescence studies showed that the alkaloids bound cooperatively to these RNAs with the binding affinities of the order 10(4) M(-1). Circular dichroic results suggested that the conformation of poly(A). poly(U) was perturbed by all the three alkaloids, that of poly(I).poly(C) by coralyne only and that of poly(C).poly(G) by none. Fluorescence quenching studies gave evidence for partial intercalation of berberine and palmatine and complete intercalation of coralyne to these RNA duplexes. Isothermal titration calorimetric studies revealed that the binding was characterized by negative enthalpy and positive entropy changes and the affinity constants derived were in agreement with the overall binding affinity from spectral data. The binding of all the three alkaloids considerably stabilized the melting of poly(A). poly(U) and poly(I).poly(C) and the binding data evaluated from the melting data were in agreement with that obtained from other techniques. The overall binding affinity of the alkaloids to these double stranded RNAs varied in the order, berberine = palmatine < coralyne. The temperature dependence of the enthalpy changes afforded large negative values of heat capacity changes for the binding of palmatine and coralyne to poly(A).poly(U) and of coralyne to poly(I).poly(C), suggesting substantial hydrophobic contribution in the binding process. Further, enthalpy-entropy compensation was also seen in almost all the systems that showed binding. These results further advance our understanding on the binding of small molecules that are specific binders to double stranded RNA sequences.
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Affiliation(s)
- Md Maidul Islam
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata 700 032, India
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118
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Kostjukov VV, Khomutova NM, Lantushenko AO, Evstigneev MP. Hydrophobic contribution to the free energy of complexation of aromatic ligands with DNA. ACTA ACUST UNITED AC 2009. [DOI: 10.7124/bc.0007d6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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119
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Islam MM, Pandya P, Kumar S, Kumar GS. RNA targeting through binding of small molecules: Studies on t-RNA binding by the cytotoxic protoberberine alkaloidcoralyne. ACTA ACUST UNITED AC 2009; 5:244-54. [DOI: 10.1039/b816480k] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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121
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Prinetti A, Loberto N, Chigorno V, Sonnino S. Glycosphingolipid behaviour in complex membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1788:184-93. [DOI: 10.1016/j.bbamem.2008.09.001] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2008] [Revised: 09/02/2008] [Accepted: 09/03/2008] [Indexed: 12/12/2022]
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122
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Meinhardt S, Swint-Kruse L. Experimental identification of specificity determinants in the domain linker of a LacI/GalR protein: bioinformatics-based predictions generate true positives and false negatives. Proteins 2008; 73:941-57. [PMID: 18536016 DOI: 10.1002/prot.22121] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In protein families, conserved residues often contribute to a common general function, such as DNA-binding. However, unique attributes for each homolog (e.g. recognition of alternative DNA sequences) must arise from variation in other functionally-important positions. The locations of these "specificity determinant" positions are obscured amongst the background of varied residues that do not make significant contributions to either structure or function. To isolate specificity determinants, a number of bioinformatics algorithms have been developed. When applied to the LacI/GalR family of transcription regulators, several specificity determinants are predicted in the 18 amino acids that link the DNA-binding and regulatory domains. However, results from alternative algorithms are only in partial agreement with each other. Here, we experimentally evaluate these predictions using an engineered repressor comprising the LacI DNA-binding domain, the LacI linker, and the GalR regulatory domain (LLhG). "Wild-type" LLhG has altered DNA specificity and weaker lacO(1) repression compared to LacI or a similar LacI:PurR chimera. Next, predictions of linker specificity determinants were tested, using amino acid substitution and in vivo repression assays to assess functional change. In LLhG, all predicted sites are specificity determinants, as well as three sites not predicted by any algorithm. Strategies are suggested for diminishing the number of false negative predictions. Finally, individual substitutions at LLhG specificity determinants exhibited a broad range of functional changes that are not predicted by bioinformatics algorithms. Results suggest that some variants have altered affinity for DNA, some have altered allosteric response, and some appear to have changed specificity for alternative DNA ligands.
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Affiliation(s)
- Sarah Meinhardt
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas 66160, USA
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123
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Bhadra K, Maiti M, Kumar GS. DNA-Binding Cytotoxic Alkaloids: Comparative Study of the Energetics of Binding of Berberine, Palmatine, and Coralyne. DNA Cell Biol 2008; 27:675-85. [DOI: 10.1089/dna.2008.0779] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Kakali Bhadra
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, India
| | - Motilal Maiti
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, India
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124
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Evidence that the bZIP domains of the Jun transcription factor bind to DNA as monomers prior to folding and homodimerization. Arch Biochem Biophys 2008; 480:75-84. [PMID: 18940179 DOI: 10.1016/j.abb.2008.10.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2008] [Revised: 10/06/2008] [Accepted: 10/07/2008] [Indexed: 01/30/2023]
Abstract
The Jun oncoprotein belongs to the AP1 family of transcription factors that is collectively engaged in diverse cellular processes by virtue of their ability to bind to the promoters of a wide spectrum of genes in a DNA sequence-dependent manner. Here, using isothermal titration calorimetry, we report detailed thermodynamics of the binding of bZIP domain of Jun to synthetic dsDNA oligos containing the TRE and CRE consensus promoter elements. Our data suggest that binding of Jun to both sites occurs with indistinguishable affinities but with distinct thermodynamic signatures comprised of favorable enthalpic contributions accompanied by entropic penalty at physiological temperatures. Furthermore, anomalously large negative heat capacity changes observed provoke a model in which Jun loads onto DNA as unfolded monomers coupled with subsequent folding and homodimerization upon association. Taken together, our data provide novel insights into the energetics of a key protein-DNA interaction pertinent to cellular signaling and cancer. Our study underscores the notion that the folding and dimerization of transcription factors upon association with DNA may be a more general mechanism employed in protein-DNA interactions and that the conventional school of thought may need to be re-evaluated.
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125
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Adhikari A, Hossain M, Maiti M, Suresh Kumar G. Energetics of the binding of phototoxic and cytotoxic plant alkaloid sanguinarine to DNA: Isothermal titration calorimetric studies. J Mol Struct 2008. [DOI: 10.1016/j.molstruc.2008.01.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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126
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Komazin-Meredith G, Petrella RJ, Santos WL, Filman DJ, Hogle JM, Verdine GL, Karplus M, Coen DM. The human cytomegalovirus UL44 C clamp wraps around DNA. Structure 2008; 16:1214-25. [PMID: 18682223 PMCID: PMC2878485 DOI: 10.1016/j.str.2008.05.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2007] [Revised: 05/02/2008] [Accepted: 05/07/2008] [Indexed: 02/02/2023]
Abstract
Processivity factors tether the catalytic subunits of DNA polymerases to DNA so that continuous synthesis of long DNA strands is possible. The human cytomegalovirus DNA polymerase subunit UL44 forms a C clamp-shaped dimer intermediate in structure between monomeric herpes simplex virus UL42, which binds DNA directly via a basic surface, and the trimeric sliding clamp PCNA, which encircles DNA. To investigate how UL44 interacts with DNA, calculations were performed in which a 12 bp DNA oligonucleotide was docked to UL44. The calculations suggested that UL44 encircles DNA, which interacts with basic residues both within the cavity of the C clamp and in flexible loops of UL44 that complete the "circle." The results of mutational and crosslinking studies were consistent with this model. Thus, UL44 is a "hybrid" of UL42 and PCNA: its structure is intermediate between the two and its mode of interaction with DNA has elements of both.
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Affiliation(s)
- Gloria Komazin-Meredith
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Robert J. Petrella
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Webster L. Santos
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - David J. Filman
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - James M. Hogle
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Gregory L. Verdine
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Martin Karplus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Laboratoire de Chimie Biophysique, ISIS, Université Louis Pasteur, 67000 Strasbourg, France
| | - Donald M. Coen
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
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127
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Menon L, Mader SA, Mihailescu MR. Fragile X mental retardation protein interactions with the microtubule associated protein 1B RNA. RNA (NEW YORK, N.Y.) 2008; 14:1644-55. [PMID: 18579868 PMCID: PMC2491469 DOI: 10.1261/rna.1100708] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Fragile X mental retardation syndrome, the most common form of inherited mental retardation, is caused by the absence of the fragile X mental retardation protein (FMRP). FMRP has been shown to use its arginine-glycine-glycine (RGG) box to bind to a subset of RNA targets that form a G quadruplex structure. We performed a detailed analysis of the interactions between the FMRP RGG box and the microtubule associated protein 1B (MAP1B) mRNA, a relevant in vivo FMRP target. We show that MAP1B RNA forms an intramolecular G quadruplex structure, which is bound with high affinity and specificity by the FMRP RGG box. We determined that hydrophobic interactions are important in the FMRP RGG box-MAP1B RNA association, with minor contributions from electrostatic interactions. Our findings that at low protein:RNA ratios the RNA G quadruplex structure is slightly stabilized, whereas at high ratios is unfolded, suggest a mechanism by which the FMRP concentration variation in response to a neurotransmitter stimulation event could act as a regulatory switch for the protein function, from translation repressor to translation activator.
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Affiliation(s)
- Lakshmi Menon
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282, USA
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128
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Shaw NN, Xi H, Arya DP. Molecular recognition of a DNA:RNA hybrid: sub-nanomolar binding by a neomycin-methidium conjugate. Bioorg Med Chem Lett 2008; 18:4142-5. [PMID: 18573660 DOI: 10.1016/j.bmcl.2008.05.090] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2008] [Revised: 05/21/2008] [Accepted: 05/21/2008] [Indexed: 11/15/2022]
Abstract
A novel neomycin-methidium conjugate was synthesized. The covalent linkage of the aminoglycoside to an intercalator, a derivative of ethidium bromide, results in a new conjugate capable of selective recognition of the DNA:RNA hybrid duplex. Spectroscopic methods: UV, CD, fluorescence, and calorimetric techniques: DSC and ITC were used to characterize the sub-nanomolar binding displayed by the conjugate for the DNA:RNA hybrid duplex, poly(dA):poly(rU).
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Affiliation(s)
- Nicholas N Shaw
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, USA
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129
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Berberine-DNA complexation: new insights into the cooperative binding and energetic aspects. Biochim Biophys Acta Gen Subj 2008; 1780:1054-61. [PMID: 18549823 DOI: 10.1016/j.bbagen.2008.05.005] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Revised: 05/16/2008] [Accepted: 05/16/2008] [Indexed: 01/31/2023]
Abstract
The equilibrium binding of the cytotoxic plant alkaloid berberine to various DNAs and energetics of the interaction have been studied. At low ratios of bound alkaloid to base pair, the binding exhibited cooperativity to natural DNAs having almost equal proportions of AT and GC sequences. In contrast, the binding was non-cooperative to DNAs with predominantly high AT or GC sequences. Among the synthetic DNAs, cooperative binding was observed with poly(dA).poly(dT) and poly(dG).poly(dC) while non-cooperative binding was seen with poly(dA-dT).poly(dA-dT) and poly(dG-dC).poly(dG-dC). Both cooperative and non-cooperative bindings were remarkably dependent on the salt concentration of the media. Linear plots of ln K(a) versus [Na(+)] for poly(dA).poly(dT) and poly(dA-dT).poly(dA-dT) showed the release of 0.56 and 0.75 sodium ions respectively per bound alkaloid. Isothermal titration calorimetry results revealed the binding to be exothermic and favoured by both enthalpy and entropy changes in all DNAs except the two AT polymers and AT rich DNA, where the same was predominantly entropy driven. Heat capacity values (DeltaCp(o)) of berberine binding to poly(dA).poly(dT), poly(dA-dT).poly(dA-dT), Clostridium perfringens and calf thymus DNA were -98, -140, -120 and -110 cal/mol K respectively. This study presents new insights into the binding dependent base pair heterogeneity in DNA conformation and the first complete thermodynamic profile of berberine binding to DNAs.
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130
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Lin PH, Yen SL, Lin MS, Chang Y, Louis SR, Higuchi A, Chen WY. Microcalorimetrics studies of the thermodynamics and binding mechanism between L-tyrosinamide and aptamer. J Phys Chem B 2008; 112:6665-73. [PMID: 18457441 DOI: 10.1021/jp8000866] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In recent years, several high-resolution structures of aptamer complexes have shed light on the binding mode and recognition principles of aptamer complex interactions. In some cases, however, the aptamer complex binding behavior and mechanism are not clearly understood, especially with the absence of structural information. In this study, it was demonstrated that isothermal titration calorimetry (ITC) and circular dichroism (CD) were useful tools for studying the fundamental binding mechanism between a DNA aptamer and L-tyrosinamide (L-TyrNH2). To gain further insight into this behavior, thermodynamic and conformational measurements under different parameters such as salt concentration, temperature, pH value, analogue of L-TyrNH2, and metal ion were carried out. The thermodynamic signature along with the coupled CD spectral change suggest that this binding behavior is an enthalpy-driven process, and the aptamer has a conformational change from B-form to A-form. The results showed that the interaction is an induced fit binding, and the driving forces in this binding behavior may include electrostatic interactions, hydrophobic effects, hydrogen bonding, and the binding-linked protonation process. The amide group and phenolic hydroxyl group of the L-TyrNH2 play a vital role in this binding mechanism. In addition, it should be noted that Mg(2+) not only improves binding affinity but also helps change the structure of the DNA aptamer.
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Affiliation(s)
- Po-Hsun Lin
- Institute of Systems Biology and Bioinformatics, National Central University, Jhong-Li, Taiwan
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131
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Liu CC, Richard AJ, Datta K, LiCata VJ. Prevalence of temperature-dependent heat capacity changes in protein-DNA interactions. Biophys J 2008; 94:3258-65. [PMID: 18199676 PMCID: PMC2275698 DOI: 10.1529/biophysj.107.117697] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2007] [Accepted: 12/18/2007] [Indexed: 11/18/2022] Open
Abstract
A large, negative DeltaCp of DNA binding is a thermodynamic property of the majority of sequence-specific DNA-protein interactions, and a common, but not universal property of non-sequence-specific DNA binding. In a recent study of the binding of Taq polymerase to DNA, we showed that both the full-length polymerase and its "Klentaq" large fragment bind to primed-template DNA with significant negative heat capacities. Herein, we have extended this analysis by analyzing this data for temperature-variable heat capacity effects (DeltaDeltaCp), and have similarly analyzed an additional 47 protein-DNA binding pairs from the scientific literature. Over half of the systems examined can be easily fit to a function that includes a DeltaDeltaCp parameter. Of these, 90% display negative DeltaDeltaCp values, with the result that the DeltaCp of DNA binding will become more negative with rising temperature. The results of this collective analysis have potentially significant consequences for current quantitative theories relating DeltaCp values to changes in accessible surface area, which rely on the assumption of temperature invariance of the DeltaCp of binding. Solution structural data for Klentaq polymerase demonstrate that the observed heat capacity effects are not the result of a coupled folding event.
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Affiliation(s)
- Chin-Chi Liu
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
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132
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Bhadra K, Maiti M, Kumar G. Interaction of Isoquinoline Alkaloid Palmatine with Deoxyribonucleic Acids: Binding Heterogeneity, and Conformational and Thermodynamic Aspects. Chem Biodivers 2008; 5:575-90. [DOI: 10.1002/cbdv.200890054] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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133
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Entropy Changes in Aqueous Solutions of Non-polar Substances and in Bio-complex Formation. J SOLUTION CHEM 2008. [DOI: 10.1007/s10953-008-9248-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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134
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Thompson M, Chandrasekaran R. Thermodynamic analysis of acetylation-dependent Pb1 bromodomain-histone H3 interactions. Anal Biochem 2008; 374:304-12. [PMID: 18191465 PMCID: PMC2693409 DOI: 10.1016/j.ab.2007.12.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2007] [Revised: 12/06/2007] [Accepted: 12/07/2007] [Indexed: 12/23/2022]
Abstract
An acetyl-histone peptide library was used to determine the thermodynamic parameters that define acetylation-dependent bromodomain-histone interactions. Bromodomains interact with histones by binding acetylated lysines. The bromodomain used in this study, BrD3, is derived from the polybromo-1 protein, which is a subunit of the PBAF chromatin remodeling complex. Steady-state fluorescence anisotropy was used to examine the variations in specificity and affinity that drive molecular recognition. Temperature and salt concentration dependence studies demonstrate that the hydrophobic effect is the primary driving force, consistent with lysine acetylation being required for binding. An electrostatic effect was observed in only two complexes where the acetyl-lysine was adjacent to an arginine. The large change in heat capacity determined for the specific complex suggests that the dehydrated BrD3-histone interface forms a tightly bound, high-affinity complex with the target site. These explorations into the thermodynamic driving forces that confer acetylation site-dependent BrD3-histone interactions improve our understanding of how individual bromodomains work in isolation. Furthermore, this work will permit the development of hypotheses regarding how the native Pb1, and the broader class of bromodomain proteins, directs multisubunit chromatin remodeling complexes to specific acetyl-nucleosome sites in vivo.
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Affiliation(s)
- Martin Thompson
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931, USA.
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135
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Coupling of folding and DNA-binding in the bZIP domains of Jun-Fos heterodimeric transcription factor. Arch Biochem Biophys 2008; 473:48-60. [PMID: 18316037 DOI: 10.1016/j.abb.2008.02.024] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2008] [Revised: 02/18/2008] [Accepted: 02/19/2008] [Indexed: 01/06/2023]
Abstract
In response to mitogenic stimuli, the heterodimeric transcription factor Jun-Fos binds to the promoters of a diverse array of genes involved in critical cellular responses such as cell growth and proliferation, cell cycle regulation, embryogenic development and cancer. In so doing, Jun-Fos heterodimer regulates gene expression central to physiology and pathology of the cell in a specific and timely manner. Here, using the technique of isothermal titration calorimetry (ITC), we report detailed thermodynamics of the bZIP domains of Jun-Fos heterodimer to synthetic dsDNA oligos containing the TRE and CRE consensus promoter elements. Our data suggest that binding of the bZIP domains to both TRE and CRE is under enthalpic control and accompanied by entropic penalty at physiological temperatures. Although the bZIP domains bind to both TRE and CRE with very similar affinities, the enthalpic contributions to the free energy of binding to CRE are more favorable than TRE, while the entropic penalty to the free energy of binding to TRE is smaller than CRE. Despite such differences in their thermodynamic signatures, enthalpy and entropy of binding of the bZIP domains to both TRE and CRE are highly temperature-dependent and largely compensate each other resulting in negligible effect of temperature on the free energy of binding. From the plot of enthalpy change versus temperature, the magnitude of heat capacity change determined is much larger than that expected from the direct association of bZIP domains with DNA. This observation is interpreted to suggest that the basic regions in the bZIP domains are largely unstructured in the absence of DNA and only become structured upon interaction with DNA in a coupled folding and binding manner. Our new findings are rationalized in the context of 3D structural models of bZIP domains of Jun-Fos heterodimer in complex with dsDNA oligos containing the TRE and CRE consensus sequences. Taken together, our study demonstrates that enthalpy is the major driving force for a key protein-DNA interaction pertinent to cellular signaling and that protein-DNA interactions with similar binding affinities may be accompanied by differential thermodynamic signatures. Our data corroborate the notion that the DNA-induced protein structural changes are a general feature of the bZIP family of transcription factors.
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136
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Bhadra K, Maiti M, Kumar GS. Thermodynamics of the binding of cytotoxic protoberberine molecule coralyne to deoxyribonucleic acids. Biochim Biophys Acta Gen Subj 2008; 1780:298-306. [DOI: 10.1016/j.bbagen.2007.11.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Revised: 11/14/2007] [Accepted: 11/30/2007] [Indexed: 11/15/2022]
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137
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Hossain M, Giri P, Kumar GS. DNA Intercalation by Quinacrine and Methylene Blue: A Comparative Binding and Thermodynamic Characterization Study. DNA Cell Biol 2008; 27:81-90. [PMID: 17924822 DOI: 10.1089/dna.2007.0652] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Maidul Hossain
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, Kolkata, West Bengal, India
| | - Prabal Giri
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, Kolkata, West Bengal, India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, Kolkata, West Bengal, India
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138
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Niedzwiecka A, Stepinski J, Antosiewicz JM, Darzynkiewicz E, Stolarski R. Biophysical approach to studies of cap-eIF4E interaction by synthetic cap analogs. Methods Enzymol 2008; 430:209-45. [PMID: 17913640 DOI: 10.1016/s0076-6879(07)30009-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Specific recognition of mRNA 5' cap by eukaryotic initiation factor eIF4E is a rate-limiting step in the translation initiation. Structural determination of the eIF4E-cap complexes, as well as complexes of eIF4E with other proteins regulating its activity, requires complementary experiments that allow for energetic and dynamic aspects of formation and stability of the complexes. Such a combined approach provides information on the binding mechanisms and, hence, may lead to mechanistic models of eIF4E functioning and regulation on the molecular level. This chapter summarizes in detail the method of experiments used to probe the cap-binding center of eIF4E, steady state and stopped-flow fluorescence, and microcalorimetry. The studies were performed with a wide class of synthetic, structurally modified cap analogs that resembles in some respect an application of site directed mutagenesis of the protein. The chapter presents a general recipe as to how to investigate protein-ligand interactions if the protein has no enzymatic activity and both the protein and the ligand absorb and emit UV/VIS radiation in the same spectral ranges.
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Affiliation(s)
- Anna Niedzwiecka
- Division of Biophysics, Institute of Experimental Physics, Warsaw University, Warszawa, Poland
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139
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Chen SH, Suzuki CK, Wu SH. Thermodynamic characterization of specific interactions between the human Lon protease and G-quartet DNA. Nucleic Acids Res 2008; 36:1273-87. [PMID: 18174225 PMCID: PMC2275097 DOI: 10.1093/nar/gkm1140] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Lon is an ATP-powered protease that binds DNA. However, the function of DNA binding by Lon remains elusive. Studies suggest that human Lon (hLon) binds preferentially to a G-rich single-stranded DNA (ssDNA) sequence overlapping the light strand promoter of mitochondrial DNA. This sequence is contained within a 24-base oligonucleotide referred to as LSPas. Here, we use biochemical and biophysical approaches to elucidate the structural properties of ssDNAs bound by hLon, as well as the thermodynamics of DNA binding by hLon. Electrophoretic mobility shift assay and circular dichroism show that ssDNAs with a propensity for forming parallel G-quartets are specifically bound by hLon. Isothermal titration calorimetry demonstrates that hLon binding to LSPas is primarily driven by enthalpy change associated with a significant reduction in heat capacity. Differential scanning calorimetry pinpoints an excess heat capacity upon hLon binding to LSPas. By contrast, hLon binding to an 8-base G-rich core sequence is entropically driven with a relatively negligible change in heat capacity. A considerable enhancement of thermal stability accompanies hLon binding to LSPas as compared to the G-rich core. Taken together, these data support the notion that hLon binds G-quartets through rigid-body binding and that binding to LSPas is coupled with structural adaptation.
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Affiliation(s)
- Si-Han Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
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140
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Tungtur S, Egan SM, Swint-Kruse L. Functional consequences of exchanging domains between LacI and PurR are mediated by the intervening linker sequence. Proteins 2007; 68:375-88. [PMID: 17436321 PMCID: PMC2084478 DOI: 10.1002/prot.21412] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Homologue function can be differentiated by changing residues that affect binding sites or long-range interactions. LacI and PurR are two proteins that represent the LacI/GalR family (>500 members) of bacterial transcription regulators. All members have distinct DNA-binding and regulatory domains linked by approximately 18 amino acids. Each homologue has specificity for different DNA and regulatory effector ligands; LacI and PurR also exhibit differences in allosteric communication between DNA and effector binding sites. A comparative study of LacI and PurR suggested that alterations in the interface between the regulatory domain and linker are important for differentiating their functions. Four residues (equivalent to LacI positions 48, 55, 58, and 61) appear particularly important for creating a unique interface and were predicted to be necessary for allosteric regulation. However, nearby residues in the linker interact with DNA ligand. Thus, differences observed in interactions between linker and regulatory domain may be the cause of altered function or an effect of the two proteins binding different DNA ligands. To separate these possibilities, we created a chimeric protein with the LacI DNA-binding domain/linker and the PurR regulatory domain (LLhP). If the interface requires homologue-specific interactions in order to propagate the signal from effector binding, then LLhP repression should not be allosterically regulated by effector binding. Experiments show that LLhP is capable of repression from lacO1 and, contrary to expectation, allosteric response is intact. Further, restoring the potential for PurR-like interactions via substitutions in the LLhP linker tends to diminish repression. These effects are especially pronounced for residues 58 and 61. Clearly, binding affinity of LLhP for the lacO1 DNA site is sensitive to long-range changes in the linker. This result also raises the possibility that mutations at positions 58 and 61 co-evolved with changes in the DNA-binding site. In addition, repression measured in the absence and presence of effector ligand shows that allosteric response increases for several LLhP variants with substitutions at positions 48 and 55. Thus, while side chain variation at these sites does not generally dictate the presence or absence of allostery, the nature of the amino acid can modulate the response to effector.
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Affiliation(s)
- Sudheer Tungtur
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas 66160
| | - Susan M. Egan
- Department of Molecular Biosciences, The University of Kansas–Lawrence, Lawrence, Kansas 66045
| | - Liskin Swint-Kruse
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas 66160
- *Correspondence to: Liskin Swint-Kruse, Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas 66160. E-mail:
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141
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Taraban M, Zhan H, Whitten AE, Langley DB, Matthews KS, Swint-Kruse L, Trewhella J. Ligand-induced conformational changes and conformational dynamics in the solution structure of the lactose repressor protein. J Mol Biol 2007; 376:466-81. [PMID: 18164724 DOI: 10.1016/j.jmb.2007.11.067] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Revised: 11/16/2007] [Accepted: 11/20/2007] [Indexed: 11/30/2022]
Abstract
We present here the results of a series of small-angle X-ray scattering studies aimed at understanding the role of conformational changes and structural flexibility in DNA binding and allosteric signaling in a bacterial transcription regulator, lactose repressor protein (LacI). Experiments were designed to detect possible conformational changes that occur when LacI binds either DNA or the inducer IPTG, or both. Our studies included the native LacI dimer of homodimers and a dimeric variant (R3), enabling us to probe conformational changes within the homodimers and distinguish them from those involving changes in the homodimer-homodimer relationships. The scattering data indicate that removal of operator DNA (oDNA) from R3 results in an unfolding and extension of the hinge helix that connects the LacI regulatory and DNA-binding domains. In contrast, only very subtle conformational changes occur in the R3 dimer-oDNA complex upon IPTG binding, indicative of small adjustments in the orientations of domains and/or subdomains within the structure. The binding of IPTG to native (tetrameric) LacI-oDNA complexes also appears to facilitate a modest change in the average homodimer-homodimer disposition. Notably, the crystal structure of the native LacI-oDNA complex differs significantly from the average solution conformation. The solution scattering data are best fit by an ensemble of structures that includes (1) approximately 60% of the V-shaped dimer of homodimers observed in the crystal structure and (2) approximately 40% of molecules with more "open" forms, such as those generated when the homodimers move with respect to each other about the tetramerization domain. In gene regulation, such a flexible LacI would be beneficial for the interaction of its two DNA-binding domains, positioned at the tips of the V, with the required two of three LacI operators needed for full repression.
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Affiliation(s)
- Marc Taraban
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
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142
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Kano K, Ishida Y, Kitagawa K, Yasuda M, Watanabe M. Heat-Capacity Changes in Host–Guest Complexation by Coulomb Interactions in Aqueous Solution. Chem Asian J 2007; 2:1305-13. [PMID: 17668911 DOI: 10.1002/asia.200700142] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Heat-capacity changes (deltaC(p)0) were determined for the complexation of 1-alkanecarboxylates with protonated hexakis(6-amino-6-deoxy)-alpha-cyclodextrin (per-NH3(+)-alpha-CD) and heptakis(6-amino-6-deoxy)-beta-cyclodextrin (per-NH3(+)-beta-CD). DeltaC(p)0 decreased with an increase in the binding constant (K) and plateaued at K = 4000 M(-1). The complexes of 1-pentanoate, 1-hexanoate, and 1-heptanoate with per-NH3(+)-alpha-CD are classified as the host-guest system in which the size of the guest fits the CD cavity well. In such a system, van der Waals interaction is the major force for complexation, leading to a negative deltaH0 value. Simultaneously, the water molecules around the hydrophobic alkyl chain of the guest and inside the CD cavity are released to the aqueous bulk phase, leading to a positive deltaS0 value. The negative deltaC(p)0 value in such complexation is ascribed to dehydration of the hydrophobic alkyl chain of the guest and extrusion of the water molecules inside the CD cavity. Meanwhile, the complexes that show positive deltaC(p)0 values are characterized by complexation in which the guest molecules are significantly smaller than the CD cavities. In such a case, the complexation is endothermic and driven by the entropy gain. When the guest is much smaller than the CD cavity, the main binding force should be Coulomb interaction. To form an ionic bond, dehydration of the charged groups must occur. This process is endothermic and leads to positive deltaH0 and deltaS0 values. As the top of the CD cavity is capped by a small but hydrophobic alkyl chain, the water molecules inside the CD cavity may form the iceberg structure. This process must be accompanied by a positive deltaC(p)0 value. Hence, the complexation of a small guest with the CD with a large cavity through Coulomb interactions shows positive and large deltaC(p)0 values. These conclusions were applied to the electrostatic binding of proteins with an anionic ligand.
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Affiliation(s)
- Koji Kano
- Department of Molecular Science and Technology, Faculty of Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan.
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143
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Sinha R, Hossain M, Kumar GS. RNA targeting by DNA binding drugs: structural, conformational and energetic aspects of the binding of quinacrine and DAPI to A-form and H(L)-form of poly(rC).poly(rG). Biochim Biophys Acta Gen Subj 2007; 1770:1636-50. [PMID: 17942232 DOI: 10.1016/j.bbagen.2007.08.018] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2007] [Revised: 08/13/2007] [Accepted: 08/23/2007] [Indexed: 11/16/2022]
Abstract
A key step in the rational design of new RNA binding small molecules necessitates a complete elucidation of the molecular aspects of the binding of existing molecules to RNA structures. This work focuses towards the understanding of the interaction of a DNA intercalator, quinacrine and a minor groove binder 4',6-diamidino-2-phenylindole (DAPI) with the right handed Watson-Crick base paired A-form and the left-handed Hoogsteen base paired H(L)-form of poly(rC).poly(rG) evaluated by multifaceted spectroscopic and viscometric techniques. The energetics of their interaction has also been elucidated by isothermal titration calorimetry. Results of this study converge to suggest that (i) quinacrine intercalates to both A-form and H(L)-form of poly(rC).poly(rG); (ii) DAPI shows both intercalative and groove-binding modes to the A-form of the RNA but binds by intercalative mode to the H(L)-form. Isothermal calorimetric patterns of quinacrine binding to both the forms of RNA and of DAPI binding to the H(L)-form are indicative of single binding while the binding of DAPI to the A-form reveals two kinds of binding. The binding of both the drugs to both conformations of RNA is exothermic; while the binding of quinacrine to both conformations and DAPI to the A-form (first site) is entropy driven, the binding of DAPI to the second site of A-form and H(L)-conformation is enthalpy driven. Temperature dependence of the binding enthalpy revealed that the RNA-ligand interaction reactions are accompanied by small heat capacity changes that are nonetheless significant. We conclude that the binding affinity characteristics and energetics of interaction of these DNA binding molecules to the RNA conformations are significantly different and may serve as data for the development of effective structure selective RNA-based antiviral drugs.
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Affiliation(s)
- Rangana Sinha
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, 4 Raja S.C. Mullick Road, Kolkata, India
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144
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Barceló F, Scotta C, Ortiz-Lombardía M, Méndez C, Salas JA, Portugal J. Entropically-driven binding of mithramycin in the minor groove of C/G-rich DNA sequences. Nucleic Acids Res 2007; 35:2215-26. [PMID: 17369273 PMCID: PMC1874653 DOI: 10.1093/nar/gkm037] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The antitumour antibiotic mithramycin A (MTA) is a DNA minor-groove binding ligand. It binds to C/G-rich tracts as a dimer that forms in the presence of divalent cations such as Mg(2+). Differential scanning calorimetry, UV thermal denaturation, isothermal titration calorimetry and competition dialysis were used, together with computations of the hydrophobic free energy of binding, to determine the thermodynamic profile of MTA binding to DNA. The results were compared to those obtained in parallel using the structurally related mithramycin SK (MSK). The binding of MTA to salmon testes DNA determined by UV melting studies (K(obs) = 1.2 (+/-0.3) x 10(5) M(-1)) is tighter than that of MSK (2.9 (+/-1.0) x 10(4) M(-1)) at 25 degrees C. Competition dialysis studies showed a tighter MTA binding to both salmon testes DNA (42% C + G) and Micrococcus lysodeikticus DNA (72% C + G). The thermodynamic analysis of binding data at 25 degrees C shows that the binding of MTA and MSK to DNA is entropically driven, dominated by the hydrophobic transfer of the antibiotics from solution to the DNA-binding site. Direct molecular recognition between MTA or MSK and DNA through hydrogen bonding and van der Waals contacts may also contribute significantly to complex formation.
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Affiliation(s)
- Francisca Barceló
- Departament de Biologia Fundamental i Ciencies de la Salut, Universitat de les Illes Balears, Palma de Mallorca, Spain, Programa de Biologia Estructural y Biocomputacion, Centro Nacional de Investigaciones Oncologicas (CNIO), Madrid, Spain, Departamento de Biologia Funcional-Instituto Universitario de Oncologia del Principado de Asturias, Oviedo, Spain and Instituto de Biologia Molecular de Barcelona, CSIC, Parc Cientific de Barcelona, Barcelona, Spain
| | - Claudia Scotta
- Departament de Biologia Fundamental i Ciencies de la Salut, Universitat de les Illes Balears, Palma de Mallorca, Spain, Programa de Biologia Estructural y Biocomputacion, Centro Nacional de Investigaciones Oncologicas (CNIO), Madrid, Spain, Departamento de Biologia Funcional-Instituto Universitario de Oncologia del Principado de Asturias, Oviedo, Spain and Instituto de Biologia Molecular de Barcelona, CSIC, Parc Cientific de Barcelona, Barcelona, Spain
| | - Miguel Ortiz-Lombardía
- Departament de Biologia Fundamental i Ciencies de la Salut, Universitat de les Illes Balears, Palma de Mallorca, Spain, Programa de Biologia Estructural y Biocomputacion, Centro Nacional de Investigaciones Oncologicas (CNIO), Madrid, Spain, Departamento de Biologia Funcional-Instituto Universitario de Oncologia del Principado de Asturias, Oviedo, Spain and Instituto de Biologia Molecular de Barcelona, CSIC, Parc Cientific de Barcelona, Barcelona, Spain
| | - Carmen Méndez
- Departament de Biologia Fundamental i Ciencies de la Salut, Universitat de les Illes Balears, Palma de Mallorca, Spain, Programa de Biologia Estructural y Biocomputacion, Centro Nacional de Investigaciones Oncologicas (CNIO), Madrid, Spain, Departamento de Biologia Funcional-Instituto Universitario de Oncologia del Principado de Asturias, Oviedo, Spain and Instituto de Biologia Molecular de Barcelona, CSIC, Parc Cientific de Barcelona, Barcelona, Spain
| | - José A. Salas
- Departament de Biologia Fundamental i Ciencies de la Salut, Universitat de les Illes Balears, Palma de Mallorca, Spain, Programa de Biologia Estructural y Biocomputacion, Centro Nacional de Investigaciones Oncologicas (CNIO), Madrid, Spain, Departamento de Biologia Funcional-Instituto Universitario de Oncologia del Principado de Asturias, Oviedo, Spain and Instituto de Biologia Molecular de Barcelona, CSIC, Parc Cientific de Barcelona, Barcelona, Spain
| | - José Portugal
- Departament de Biologia Fundamental i Ciencies de la Salut, Universitat de les Illes Balears, Palma de Mallorca, Spain, Programa de Biologia Estructural y Biocomputacion, Centro Nacional de Investigaciones Oncologicas (CNIO), Madrid, Spain, Departamento de Biologia Funcional-Instituto Universitario de Oncologia del Principado de Asturias, Oviedo, Spain and Instituto de Biologia Molecular de Barcelona, CSIC, Parc Cientific de Barcelona, Barcelona, Spain
- *To whom correspondence should be addressed. +34 93 403 4959+34 93 403 4979
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145
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Shi X, Macgregor RB. Volume and hydration changes of DNA–ligand interactions. Biophys Chem 2007; 125:471-82. [PMID: 17112653 DOI: 10.1016/j.bpc.2006.10.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2006] [Revised: 10/25/2006] [Accepted: 10/25/2006] [Indexed: 10/23/2022]
Abstract
We report the volumetric and other thermodynamic properties of ethidium bromide (EB), propidium iodide (PI) and daunomycin (DAU) intercalating with poly(dA).poly(dT), poly[d(A-T)].poly[d(A-T)], and poly[d(G-C)].poly[d(G-C)], respectively, as well as minor groove binder Hoechst 33258 binding with poly[d(A-T)].poly[d(A-T)]. The data were obtained using fluorescence titration and hydrostatic pressure measurements. Our thermodynamic data are combined with enthalpies from literature reports to analyze the thermodynamic characteristics of the different interactions. The differences are interpreted based on three processes related to hydration: I. burial of non-polar hydrophobic solvent accessible surface, II. burial of polar surface and formation of solute-solute H-bonds, and III. disruption of "structural" hydration. Sequence dependent conformational changes may also be important when comparing ligand binding to different DNA sequences. We conclude that a combination of different thermodynamic parameters, especially volume change, is essential in order to understand the role of hydration in the energetics of DNA-ligand interactions.
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Affiliation(s)
- Xuesong Shi
- Leslie Dan Faculty of Pharmacy, University of Toronto, Canada
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146
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Energetics of the protein-DNA-water interaction. BMC STRUCTURAL BIOLOGY 2007; 7:4. [PMID: 17214883 PMCID: PMC1781455 DOI: 10.1186/1472-6807-7-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2006] [Accepted: 01/10/2007] [Indexed: 11/30/2022]
Abstract
Background To understand the energetics of the interaction between protein and DNA we analyzed 39 crystallographically characterized complexes with the HINT (Hydropathic INTeractions) computational model. HINT is an empirical free energy force field based on solvent partitioning of small molecules between water and 1-octanol. Our previous studies on protein-ligand complexes demonstrated that free energy predictions were significantly improved by taking into account the energetic contribution of water molecules that form at least one hydrogen bond with each interacting species. Results An initial correlation between the calculated HINT scores and the experimentally determined binding free energies in the protein-DNA system exhibited a relatively poor r2 of 0.21 and standard error of ± 1.71 kcal mol-1. However, the inclusion of 261 waters that bridge protein and DNA improved the HINT score-free energy correlation to an r2 of 0.56 and standard error of ± 1.28 kcal mol-1. Analysis of the water role and energy contributions indicate that 46% of the bridging waters act as linkers between amino acids and nucleotide bases at the protein-DNA interface, while the remaining 54% are largely involved in screening unfavorable electrostatic contacts. Conclusion This study quantifies the key energetic role of bridging waters in protein-DNA associations. In addition, the relevant role of hydrophobic interactions and entropy in driving protein-DNA association is indicated by analyses of interaction character showing that, together, the favorable polar and unfavorable polar/hydrophobic-polar interactions (i.e., desolvation) mostly cancel.
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147
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Sonnino S, Mauri L, Chigorno V, Prinetti A. Gangliosides as components of lipid membrane domains. Glycobiology 2006; 17:1R-13R. [PMID: 16982663 DOI: 10.1093/glycob/cwl052] [Citation(s) in RCA: 258] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cell membrane components are organized as specialized domains involved in membrane-associated events such as cell signaling, cell adhesion, and protein sorting. These membrane domains are enriched in sphingolipids and cholesterol but display a low protein content. Theoretical considerations and experimental data suggest that some properties of gangliosides play an important role in the formation and stabilization of specific cell lipid membrane domains. Gangliosides are glycolipids with strong amphiphilic character and are particularly abundant in the plasma membranes, where they are inserted into the external leaflet with the hydrophobic ceramide moiety and with the oligosaccharide chain protruding into the extracellular medium. The geometry of the monomer inserted into the membrane, largely determined by the very large surface area occupied by the oligosaccharide chain, the ability of the ceramide amide linkage to form a network of hydrogen bonds at the water-lipid interface of cell membranes, the Delta(4) double bond of sphingosine proximal to the water-lipid interface, the capability of the oligosaccharide chain to interact with water, and the absence of double bonds into the double-tailed hydrophobic moiety are the ganglioside features that will be discussed in this review, to show how gangliosides are responsible for the formation of cell lipid membrane domains characterized by a strong positive curvature.
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Affiliation(s)
- Sandro Sonnino
- Department of Medical Chemistry, Biochemistry, and Biotechnology, Center of Excellence on Neurodegenerative Disease, University of Milan, 20090 Segrate (MI), Italy.
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148
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McElroy CA, Manfredo A, Gollnick P, Foster MP. Thermodynamics of tryptophan-mediated activation of the trp RNA-binding attenuation protein. Biochemistry 2006; 45:7844-53. [PMID: 16784236 PMCID: PMC2517159 DOI: 10.1021/bi0526074] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The trp RNA-binding attenuation protein (TRAP) functions in many bacilli to control the expression of the tryptophan biosynthesis genes. Transcription of the trp operon is controlled by TRAP through an attenuation mechanism, in which competition between two alternative secondary-structural elements in the 5' leader sequence of the nascent mRNA is influenced by tryptophan-dependent binding of TRAP to the RNA. Previously, NMR studies of the undecamer (11-mer) suggested that tryptophan-dependent control of RNA binding by TRAP is accomplished through ligand-induced changes in protein dynamics. We now present further insights into this ligand-coupled event from hydrogen/deuterium (H/D) exchange analysis, differential scanning calorimetry (DSC), and isothermal titration calorimetry (ITC). Scanning calorimetry showed tryptophan dissociation to be independent of global protein unfolding, while analysis of the temperature dependence of the binding enthalpy by ITC revealed a negative heat capacity change larger than expected from surface burial, a hallmark of binding-coupled processes. Analysis of this excess heat capacity change using parameters derived from protein folding studies corresponds to the ordering of 17-24 residues per monomer of TRAP upon tryptophan binding. This result is in agreement with qualitative analysis of residue-specific broadening observed in TROSY NMR spectra of the 91 kDa oligomer. Implications for the mechanism of ligand-mediated TRAP activation through a shift in a preexisting conformational equilibrium and an induced-fit conformational change are discussed.
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Affiliation(s)
- Craig A McElroy
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA
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149
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Rau DC. Sequestered water and binding energy are coupled in complexes of lambda Cro repressor with non-consensus binding sequences. J Mol Biol 2006; 361:352-61. [PMID: 16828799 DOI: 10.1016/j.jmb.2006.06.036] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2006] [Revised: 06/07/2006] [Accepted: 06/14/2006] [Indexed: 11/28/2022]
Abstract
We use the osmotic pressure dependence of dissociation rates and relative binding constants to infer differences in sequestered water among complexes of lambda Cro repressor with varied DNA recognition sequences. For over a 1000-fold change in association constant, the number of water molecules sequestered by non-cognate complexes varies linearly with binding free energy. One extra bound water molecule is coupled with the loss of approximately 150 cal/mol complex in binding free energy. Equivalently, every tenfold decrease in binding constant at constant salt and temperature is associated with eight to nine additional water molecules sequestered in the non-cognate complex. The relative insensitivity of the difference in water molecules to the nature of the osmolyte used to probe the reaction suggests that the water is sterically sequestered. If the previously measured changes in heat capacity for lambda Cro binding to different non-cognate sequences are attributed solely to this change in water, then the heat capacity change per incorporated water is almost the same as the difference between ice and water. The associated changes in enthalpies and entropies, however, indicate that the change in complex structure involves more than a simple incorporation of fixed water molecules that act as adaptors between non-complementary surfaces.
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Affiliation(s)
- Donald C Rau
- Laboratory of Physical and Structural Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
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150
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Sonnino S, Prinetti A, Mauri L, Chigorno V, Tettamanti G. Dynamic and Structural Properties of Sphingolipids as Driving Forces for the Formation of Membrane Domains. Chem Rev 2006; 106:2111-25. [PMID: 16771445 DOI: 10.1021/cr0100446] [Citation(s) in RCA: 138] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sandro Sonnino
- Center of Excellence on Neurodegenerative Diseases, Department of Medical Chemistry, Biochemistry and Biotechnology, University of Milan, 20090 Segrate (MI), Italy.
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