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Fang YY, Lipkowitz KB, Long EC. Molecular Dynamics Simulations of the Orientation of Ni(II)•Gly-Gly-His and Ni(II)•Arg-Gly-His Metallopeptide-DNA Association. J Chem Theory Comput 2015; 2:1453-63. [PMID: 26626853 DOI: 10.1021/ct600074r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Ni(II)•Xaa-Gly-His metallopeptides (where Xaa is any α-amino acid) bind selectively to the minor groove of A/T-rich DNA regions as a function of their amino acid composition and chirality. Molecular dynamics simulations were performed to clarify the most likely binding orientations of Ni(II)•Gly-Gly-His and Ni(II)•L-Arg-Gly-His upon association with the B-form oligonucleotide d(CGCGAATTCGCG)2. Upon examination of four possible docking orientations (I-IV), these studies indicated that both metallopeptides favor association with DNA via I, involving insertion of the edge of the metallopeptide containing the amino-terminal N-H and the imidazole pyrrole N-H group of His into the minor groove. These metallopeptide moieties play important roles in this DNA recognition mode by functioning as H-bond donors to minor groove acceptors such as the N3 of adenine or the O2 of thymine located on the floor of the minor groove. The positively charged side chain of L-Arg was found to enhance DNA recognition relative to that exhibited by Ni(II)•Gly-Gly-His through an increased electrostatic interaction, its favorable stereochemistry, and by providing a third point of contact with the minor groove floor. The simulation of orientation I was found to reproduce the experimentally supported DNA-metallopeptide orientation, revealing factors that are important for the further development of DNA-binding ligands.
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Affiliation(s)
- Ya-Yin Fang
- Department of Biochemistry and Molecular Biology and Department of Chemistry, Howard University, 520 W Street, NW, Washington, D.C. 20059, and Department of Chemistry and Chemical Biology, Purdue School of Science, Indiana University [Formula: see text] Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana 46202-3274
| | - Kenny B Lipkowitz
- Department of Biochemistry and Molecular Biology and Department of Chemistry, Howard University, 520 W Street, NW, Washington, D.C. 20059, and Department of Chemistry and Chemical Biology, Purdue School of Science, Indiana University [Formula: see text] Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana 46202-3274
| | - Eric C Long
- Department of Biochemistry and Molecular Biology and Department of Chemistry, Howard University, 520 W Street, NW, Washington, D.C. 20059, and Department of Chemistry and Chemical Biology, Purdue School of Science, Indiana University [Formula: see text] Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana 46202-3274
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2
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Bruce CD, Ferrara MM, Manka JL, Davis ZS, Register J. Dynamic hydrogen bonding and DNA flexibility in minor groove binders: molecular dynamics simulation of the polyamide f-ImPyIm bound to the Mlu1 (MCB) sequence 5'-ACGCGT-3' in 2:1 motif. J Mol Recognit 2015; 28:325-37. [PMID: 25711379 DOI: 10.1002/jmr.2448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 10/10/2014] [Accepted: 11/09/2014] [Indexed: 12/28/2022]
Abstract
Molecular dynamics simulations of the DNA 10-mer 5'-CCACGCGTGG-3' alone and complexed with the formamido-imidazole-pyrrole-imidazole (f-ImPyIm) polyamide minor groove binder in a 2:1 fashion were conducted for 50 ns using the pbsc0 parameters within the AMBER 12 software package. The change in DNA structure upon binding of f-ImPyIm was evaluated via minor groove width and depth, base pair parameters of Slide, Twist, Roll, Stretch, Stagger, Opening, Propeller, and x-displacement, dihedral angle distributions of ζ, ε, α, and γ determined using the Curves+ software program, and hydrogen bond formation. The dynamic hydrogen bonding between the f-ImPyIm and its cognate DNA sequence was compared to the static image used to predict sequence recognition by polyamide minor groove binders. Many of the predicted hydrogen bonds were present in less than 50% of the simulation; however, persistent hydrogen bonds between G5/15 and the formamido group of f-ImPyIm were observed. It was determined that the DNA is wider in the Complex than without the polyamide binder; however, there is flexibility in this particular sequence, even in the presence of the f-ImPyIm as evidenced by the range of minor groove widths the DNA exhibits and the dynamics of the hydrogen bonding that binds the two f-ImPyIm ions to the minor groove. The Complex consisting of the DNA and the 2 f-ImPyIm binders shows slight fraying of the 5' end of the 10-mer at the end of the simulation, but the portion of the oligomer responsible for recognition and binding is stable throughout the simulation. Several structural changes in the Complex indicate that minor groove binders may have a more active role in inhibiting transcription than just preventing binding of important transcription factors.
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Affiliation(s)
- Chrystal D Bruce
- Department of Chemistry, John Carroll University, 1 John Carroll Boulevard, University Heights, OH, 44118, USA
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3
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Khesbak H, Savchuk O, Tsushima S, Fahmy K. The Role of Water H-Bond Imbalances in B-DNA Substate Transitions and Peptide Recognition Revealed by Time-Resolved FTIR Spectroscopy. J Am Chem Soc 2011; 133:5834-42. [DOI: 10.1021/ja108863v] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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4
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Kahn TR, Fong KK, Jordan B, Lek JC, Levitan R, Mitchell PS, Wood C, Hatcher ME. An FTIR investigation of flanking sequence effects on the structure and flexibility of DNA binding sites. Biochemistry 2009; 48:1315-21. [PMID: 19166330 DOI: 10.1021/bi8015235] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fourier transform infrared (FTIR) spectroscopy and a library of FTIR marker bands have been used to examine the structure and relative flexibilities conferred by different flanking sequences on the EcoRI binding site. This approach allowed us to examine unique peaks and subtle changes in the spectra of d(AAAGAATTCTTT)(2), d(TTCGAATTCGAA)(2), and d(CGCGAATTCGCG)(2) and thereby identify local changes in base pairing, base stacking, backbone conformation, glycosidic bond rotation, and sugar puckering in the studied sequences. The changes in flanking sequences induce differences in the sugar puckers, glycosidic bond rotation, and backbone conformations. Varying levels of local flexibility are observed within the sequences in agreement with previous biological activity assays. The results also provide supporting evidence for the presence of a splay in the G(4)-C(9) base pair of the EcoRI binding site and a potential pocket of flexibility at the G(4) cleavage site that have been proposed in the literature. In sum, we have demonstrated that FTIR is a powerful methodology for studying the effect of flanking sequences on DNA structure and flexibility, for it can provide information about the local structure of the nucleic acid and the overall relative flexibilities conferred by different flanking sequences.
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Affiliation(s)
- Talia R Kahn
- Joint Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, USA
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5
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MacKerell AD. Contribution of the intrinsic mechanical energy of the phosphodiester linkage to the relative stability of the A, BI, and BII forms of duplex DNA. J Phys Chem B 2009; 113:3235-44. [PMID: 19708270 PMCID: PMC2784611 DOI: 10.1021/jp8102782] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Canonical forms of duplex DNA are known to sample well-defined regions of the alpha, beta, gamma, epsilon, and zeta dihedral angles that define the conformation of the phosphodiester linkage in the backbone of oligonucleotides. While extensive studies of base composition and base sequence dependent effects on the sampling of the A, B1, and BII canonical forms of duplex DNA have been presented, our understanding of the intrinsic contribution of the five dihedral degrees of freedom associated with the phosphodiester linkage to the conformational properties of duplex DNA is still limited. To better understand this contribution, ab initio quantum mechanical (QM) calculations were performed on a model compound representative of the phosphodiester backbone to systematically sample the energetics about the alpha, beta, gamma, epsilon, and zeta dihedral angles relevant to the conformational properties of duplex DNA. Low-energy regions of dihedral potential energy surfaces are shown to correlate with the regions of dihedral space sampled in experimental crystal structures of the canonical forms of DNA, validating the utility of the model compound and emphasizing the contribution of the intrinsic mechanical properties of the phosphodiester backbone to the conformational properties of duplex DNA. Those contributions include the relative stability of the A, BI, and BII conformations of duplex DNA, where the gas-phase energetics favor the BI form over the A and BII forms. In addition, subtle features of the potential energy surfaces mimic changes in the probability distributions of alpha, beta, gamma, epsilon, and zeta dihedral angles in A, BI, and BII forms of DNA as well as with conformations sampled in single-stranded DNA. These results show that the intrinsic mechanical properties of the phosphodiester backbone make a significant contribution to conformational properties of duplex DNA observed in the condensed phase and allow for the prediction that single-stranded DNA primarily samples folded conformations thereby possibly lowering the entropic barrier to the formation of duplex DNA.
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Affiliation(s)
- Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201, USA.
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6
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René B, Masliah G, Antri SE, Fermandjian S, Mauffret O. Conformations and Dynamics of the Phosphodiester Backbone of a DNA Fragment That Bears a Strong Topoisomerase II Cleavage Site. J Phys Chem B 2007; 111:4235-43. [PMID: 17391020 DOI: 10.1021/jp0683115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The dynamics of the DNA phosphodiester backbone conformations have been studied for a strong topoisomerase II cleavage site (site 22) using molecular dynamics simulations in explicit water and in the presence of sodium ions. We investigated the backbone motions and more particularly the BI/BII transitions involving the epsilon and zeta angles. The consensus cleavage site is adjacent to the phosphate which shows the most important phosphodiester backbone flexibility in the sequence. We infer that these latter properties could be responsible for the preferential cleavage at this site possibly through the perturbation of the cleavage/ligation activities of the topoisomerase II. More generally, the steps pur-pur and pyr-pur are those presenting the highest BII contents. Relations are observed between the backbone phosphodiester BI/BII transitions and the flexibility of the deoxyribose sugar and the helical parameters such as roll. The roll is sequence dependent when the related phosphate is in the BI form, whereas this appears not to be true when it is in the BII form. The BI/BII transitions are associated with water migration, and new relations are observed with counterions. Indeed, it is observed that a strong coupling exists between the BII form and the presence of sodium ions near the adjacent sugar deoxyribose. The presence of sodium ions in the O4' surroundings or their binding could assist the BI to BII transition by furnishing energy. The implications of these new findings and, namely, their importance in the context of the sequence-dependent behavior of BI/BII transitions will be investigated in future studies.
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Affiliation(s)
- Brigitte René
- UMR 8113 CNRS, Laboratoire de Biotechnologies et Pharmacologie Génétique Appliquée (Ecole Normale Supérieure de Cachan), Institut Gustave Roussy, 39 rue Camille Desmoulins, 94805 Villejuif Cedex, France
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7
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Fang YY, Claussen CA, Lipkowitz KB, Long EC. Diastereoselective DNA cleavage recognition by Ni(II) x Gly-Gly-His-derived metallopeptides. J Am Chem Soc 2006; 128:3198-207. [PMID: 16522100 PMCID: PMC2538425 DOI: 10.1021/ja0569757] [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
Site-selective DNA cleavage by diastereoisomers of Ni(II) x Gly-Gly-His-derived metallopeptides was investigated through high-resolution gel analyses and molecular dynamics simulations. Ni(II) x L-Arg-Gly-His and Ni(II) x D-Arg-Gly-His (and their respective Lys analogues) targeted A/T-rich regions; however, the L-isomers consistently modified a subset of available nucleotides within a given minor groove site, while the D-isomers differed in both their sites of preference and their ability to target individual nucleotides within some sites. In comparison, Ni(II) x L-Pro-Gly-His and Ni(II) x D-Pro-Gly-His were unable to exhibit a similar diastereoselectivity. Simulations of the above systems, along with Ni(II) x Gly-Gly-His, indicated that the stereochemistry of the amino-terminal amino acid produces either an isohelical metallopeptide that associates stably at individual DNA sites (L-Arg or L-Lys) or, with D-Arg and D-Lys, a noncomplementary metallopeptide structure that cannot fully employ its side chain nor amino-terminal amine as positional stabilizing moieties. In contrast, amino-terminal Pro-containing metallopeptides of either stereochemistry, lacking an extended side chain directed toward the minor groove, did not exhibit a similar diastereoselectivity. While the identity and stereochemistry of amino acids located in the amino-terminal peptide position influenced DNA cleavage, metallopeptide diastereoisomers containing L- and D-Arg (or Lys) within the second peptide position did not exhibit diastereoselective DNA cleavage patterns; simulations indicated that a positively charged amino acid in this location alters the interaction of the metallopeptide equatorial plane and the minor groove leading to an interaction similar to Ni(II) x Gly-Gly-His.
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Affiliation(s)
- Ya-Yin Fang
- Department of Chemistry & Chemical Biology, Purdue School of Science, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202-3274, USA
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8
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Madhumalar A, Bansal M. Sequence preference for BI/BII conformations in DNA: MD and crystal structure data analysis. J Biomol Struct Dyn 2005; 23:13-27. [PMID: 15918673 DOI: 10.1080/07391102.2005.10507043] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Deciphering sequence information from sugar-phosphate backbone is finely tuned through the conformational substates of DNA. BII conformation, one of the conformational substates of B-DNA, is known to play a key role in DNA-protein recognition. BI and BII are identified by the epsilon-zeta difference, which is negative in BI and positive in BII. Our analysis of MD and crystal structures shows that BII conformation is sequence specific and dinucleotides GC, CG, CA, TG, TA show high preference to take up BII conformation, while TT, TC, CT, CC dinucleotides rarely take up this conformation. Significant changes were observed in the dinucleotide parameters viz. twist, roll, and slide for the steps having BII conformation. Interestingly, the magnitude of variation in the dinucleotide parameters is seen to depend mainly on two factors, the magnitude of epsilon-zeta difference and the presence or absence of BII conformation in the second strand, across the WC base-paired dinucleotide step. Based on these two factors, the conformational substate of a dinucleotide step can be further classified as BI.BI (BI conformation in both strands), BI.BII (BI conformation in one strand and BII conformation in the other), and BII.BII (BII conformation in both strands). The occurrence of BII in both strands was found to be quite rare and thus, it can be concluded that BI.BI and BI.BII hybrid steps are more favorable than a BII.BII step. In conformity with the sequence preference seen for dinucleotides in each strand, BII.BII combination of backbone conformation was observed only for GC, CG, CA, and TG containing dinucleotide steps. We further classified BII.BII step as strong BII and weak BII depending on the magnitude of the average epsilon-zeta difference. The dinucleotide steps which belong to the category of strong BII, have large twist, high positive slide and negative roll values, while those in the weak BII group have roll, twist, and slide values similar to that of hybrid BI.BII steps. This conformational property could be contributing to the groove opening/closing and thus can modulate protein-DNA interaction.
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Affiliation(s)
- A Madhumalar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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9
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Rauch C, Pichler A, Trieb M, Wellenzohn B, Liedl KR, Mayer E. Z-DNA's conformer substates revealed by FT-IR difference spectroscopy of nonoriented left-handed double helical poly(dG-dC). J Biomol Struct Dyn 2005; 22:595-614. [PMID: 15702931 DOI: 10.1080/07391102.2005.10507029] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Nonoriented hydrated films of double helical poly(dG-dC) in the Z-form were studied by Fourier transform infrared (FT-IR) spectroscopy either as equilibrated slow-cooled samples between 290 and 220 K or, after quenching into the glassy state, as nonequilibrated film isothermally at 200, 220, and 240 K. IR spectral changes on isothermal relaxation at 200 and 220 K toward equilibrium, caused by interconversion of two conformer substates (CS) called Z1 and Z2, are revealed by IR difference spectra. Pronounced spectral changes on Z1-to-Z2 interconversion occur between approximately 750-1250 cm(-1) and these are attributed to structural changes of the phosphodiester-sugar backbone caused by changes of torsion angles, and to decreasing hydrogen-bonding of the ionic phosphate group with water molecules. These spectral changes on Z1-to-Z2 transition can be related to structural differences between ZI and ZII CS observed in single crystals. ZI/ZII CS occurs only at (dGpdC) base steps, and similar behavior is assumed for Z1/Z2. The Z1/Z2 population ratio was determined via curve resolution of marker bands for Z1 and Z2 centered at 785 and 779 cm(-1). This ratio is 0.64 at 290 K, corresponding to 39% of the phosphates of the (dGpdC) base steps in Z1 and 61% in Z2, and it increases to 1.24 on cooling to 220 K. For the Z2<=>Z1 equilibrium, an enthalpy change of -4.9 +/- 0.2 kJ mol(dGpdC)(-1) is obtained from the temperature dependence of the equilibrium constant. Z1 interconverts into Z2 at isothermal relaxation at 200 and 220 K, whereas on slow cooling from ambient temperature, Z2 interconverts into Z1. This unexpected reversal of CS interconversion is attributed to slow restructuring of hydration shells of the CS on quenching, in the same manner reported by Pichler et al. for the BI and BII CS of B-DNA (J. Phys. Chem. B 106, 3263-3274 (2002)). IR difference curves demonstrate two time scales on isothermal relaxation of Z1-->Z2 interconversion, a fast one for structural relaxation of the sugar-phosphate backbone, and a slow one for relaxation of the hydration shells. This slowing down of restructuring of CS hydration shells at approximately 220-240 K could be the cause for the suppression of biological functions at low temperatures.
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Affiliation(s)
- Christine Rauch
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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Wibowo FR, Trieb M, Rauch C, Wellenzohn B, Liedl KR. The N6-Methyl Group of Adenine Further Increases the BI Stability of DNA Compared to C5-Methyl Groups. J Phys Chem B 2004; 109:557-64. [PMID: 16851047 DOI: 10.1021/jp048519v] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Methylated DNA bases are natural modifications which play an important role in protein-DNA interactions. Recent experimental and theoretical results have shown an influence of the base modification on the conformational behavior of the DNA backbone. MD simulations of four different B-DNA dodecamers (d(GC)(6), d(AT)(6), d(G(5mCG)(5)C), and d(A(T6mA)(5)T)) have been performed with the aim to examine the influence of methyl groups on the B-DNA backbone behavior. An additional control simulation of d(AU)(6) has also been performed to examine the further influence of the C5-methyl group in thymine. Methyl groups in the major groove (as in C5-methylcytosine, thymine, or N6-methyladenine) decrease the BII substate population of RpY steps. Due to methylation a clearer distinction of the BI substate stability between YpR and RpY (CpG/GpC or TpA/ApT) steps arises. A positive correlation between the BII substate population and base stacking distances is seen only for poly(GC). A methyl group added into the major groove increases mean water residence times around the purine N7 atom, which may stabilize the BI substate by improving the hydration network between the DNA backbone and the major groove. The N6-methyl group also forms a water molecule bridge between the N6 and O4 atoms, and thus further stabilizes the BI substate.
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Affiliation(s)
- Fajar R Wibowo
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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11
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Anthony NG, Johnston BF, Khalaf AI, MacKay SP, Parkinson JA, Suckling CJ, Waigh RD. Short Lexitropsin that Recognizes the DNA Minor Groove at 5‘-ACTAGT-3‘: Understanding the Role of Isopropyl-thiazole. J Am Chem Soc 2004; 126:11338-49. [PMID: 15355117 DOI: 10.1021/ja030658n] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Isopropyl-thiazole ((iPr)Th) represents a new addition to the building blocks of nucleic acid minor groove-binding molecules. The DNA decamer duplex d(CGACTAGTCG)(2) is bound by a short lexitropsin of sequence formyl-PyPy(iPr)Th-Dp (where Py represents N-methyl pyrrole, (iPr)Th represents thiazole with an isopropyl group attached, and Dp represents dimethylaminopropyl). NMR data indicate ligand binding in the minor groove of DNA to the sequence 5'-ACT(5)AG(7)T-3' at a 2:1 ratio of ligand to DNA duplex. Ligand binding, assisted by the enhanced hydrophobicity of the (iPr)Th group, occurs in a head-to-tail fashion, the formyl headgroups being located toward the 5'-ends of the DNA sequence. Sequence reading is augmented through hydrogen bond formation between the exocyclic amine protons of G(7) and the (iPr)Th nitrogen, which lies on the minor groove floor. The B(I)/B(II) DNA backbone equilibrium is altered at the T(5) 3'-phosphate position to accommodate a B(II) configuration. The ligands bind in a staggered mode with respect to one another creating a six base pair DNA reading frame. The introduction of a new DNA sequence-reading element into the recognition jigsaw, combined with an extended reading frame for a small lexitropsin with enhanced hydrophobicity, holds great promise in the development of new, potentially commercially viable drug lead candidates for gene targeting.
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Affiliation(s)
- Nahoum G Anthony
- Department of Pure and Applied Chemistry, 295 Cathedral Street, Glasgow G1 1XL, UK
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12
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Fang YY, Ray BD, Claussen CA, Lipkowitz KB, Long EC. Ni(II)·Arg-Gly-His−DNA Interactions: Investigation into the Basis for Minor-Groove Binding and Recognition. J Am Chem Soc 2004; 126:5403-12. [PMID: 15113212 DOI: 10.1021/ja049875u] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A study of the minor-groove recognition of A/T-rich DNA sites by Ni(II).L-Arg-Gly-His and Ni(II).D-Arg-Gly-His was carried out with a fluorescence-based binding assay, one- and two-dimensional (1D and 2D) NMR methodologies, and molecular simulations. Fluorescence displacement titrations revealed that Ni(II).L-Arg-Gly-His binds to A/T-rich sequences better than the D-Arg diastereomer, while NMR investigations revealed that both metallopeptides bind to the minor groove of an AATT core region as evidenced by an intermolecular nuclear Overhauser effect (NOE) between each metallopeptide His imidazole C4 proton and the C2 proton of adenine. Results from molecular dynamics simulations of these systems were consistent with the experimental data and indicated that the His imidazole N-H, the N-terminal peptide amine, and Arg side chains of each metallopeptide are major determinants of minor-groove recognition by functioning as H-bond donors to the O2 of thymine residues or N3 of adenine residues.
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Affiliation(s)
- Ya-Yin Fang
- Department of Chemistry, Purdue School of Science, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, USA
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13
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Trieb M, Rauch C, Wellenzohn B, Wibowo F, Loerting T, Liedl KR. Dynamics of DNA: BI and BII Phosphate Backbone Transitions. J Phys Chem B 2004. [DOI: 10.1021/jp037079p] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michael Trieb
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Christine Rauch
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Bernd Wellenzohn
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Fajar Wibowo
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Thomas Loerting
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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14
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Pichler A, Rauch C, Flader W, Wellenzohn B, Liedl KR, Hallbrucker A, Mayer E. The conformer substates of nonoriented B-type DNA in double helical poly(dG-dC). J Biomol Struct Dyn 2003; 20:547-59. [PMID: 12529153 DOI: 10.1080/07391102.2003.10506871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
A nonoriented hydrated film of poly(dG-dC) with ?20 water molecules per nucleotide (called B* by Loprete and Hartman (Biochem. 32, 4077-4082 (1993)) was studied by Fourier transform infrared (FT-IR) spectroscopy either as equilibrated sample between 290 and 270 K or, after quenching into the glassy state, as nonequilibrated film isothermally at 200 and 220 K. IR spectral changes on isothermal relaxation at 200 and 220 K, caused by interconversion of two conformer substates, are revealed by difference spectra. Comparison with difference curves obtained in the same manner from two classical B-DNA forms, namely the d(CGCGAATTCGCG)(2) dodecamer and polymeric NaDNA from salmon testes, revealed that the spectral changes on B(I)-to-B(II) interconversion in the classical B-DNA forms are very similar to those in the B*-form, and that the spectroscopic differences between the B(I) and B(II) features from classical B-DNA and those from the modified B*-form are minor. Nonexponential kinetics of the B(I)-->B(II) transition in the B*-form of poly(dG-dC) at 200 K showed that the structural relaxation time is about three times of that in the classical B-DNA forms (approximately equal to 30 versus approximately equal to 10 min at 200 K). The unexpected reversal of conformer substates interconversion (that is B(II)-->B(I) transition on cooling from 290 K and B(I)-->B(II) transition on isothermal relaxation at 200 K) observed for classical B-DNA occurs also in the modified B*-form. We therefore conclude that restructuring of hydration shells rules the low-temperature dynamics of the B*-form via its two conformer substates in the same manner reported for classical B-DNA by Pichler et al. (J. Phys. Chem. B 106, 3263-3274 (2002)).
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Affiliation(s)
- Arthur Pichler
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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Flader W, Wellenzohn B, Winger RH, Hallbrucker A, Mayer E, Liedl KR. Stepwise induced fit in the pico- to nanosecond time scale governs the complexation of the even-skipped transcriptional repressor homeodomain to DNA. Biopolymers 2003; 68:139-49. [PMID: 12548619 DOI: 10.1002/bip.10242] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Induced fit effects in the complex of a DNA decamer with two even-skipped transcriptional repressor homeodomain molecules were investigated by means of molecular dynamics simulations. Dynamics of these effects are found to be in the time scale from pico- to nanoseconds. First steps are made by the fast-moving DNA backbone phosphates, which upon binding change their B(I)/B(II) substate distribution. Further rearrangements in the DNA double helix induced upon complexation, like bending of the helix axis, changes of the minor groove width, and of different helical parameters, are slower and occur within a few nanoseconds. The flexibility of the DNA, especially of its backbone, seems thereby to play an important role for specific DNA ligand recognition.
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Affiliation(s)
- Wolfgang Flader
- Institute of General, Inorganic and Theoretical Chemistry University of Innsbruck, Innrain 52a, A-6020 Innsbruck, Austria
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Rauch C, Trieb M, Flader W, Wellenzohn B, Winger RH, Mayer E, Hallbrucker A, Liedl KR. PvuII-endonuclease induces structural alterations at the scissile phosphate group of its cognate DNA. J Mol Biol 2002; 324:491-500. [PMID: 12445784 DOI: 10.1016/s0022-2836(02)01089-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We investigated the PvuII endonuclease with its cognate DNA by means of molecular dynamics simulations. Comparing the complexed DNA with a reference simulation of free DNA, we saw structural changes at the scissile phosphodiester bond. At this GpC step, the enzyme induces the highest twist and axial rise, inclination is increased and the minor groove widened. The distance between the scissile phosphate group and the phosphate group of the following thymine base is shortened significantly, indicating a substrate-assisted catalysis. A feasible reason for this vicinity is the catalytically important amino acid residue lysine 70, which bridges the free oxygen atoms of the successive phosphate groups. Due to this geometry, a compact reaction pocket is formed where a water molecule can be held, thus bringing the reaction partners for hydrolysis into contact. The O1-P-O2 angle of the scissile nucleotide is decreased, probably due to a complexation of the negative oxygen atoms through protein and solvent contacts.
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Affiliation(s)
- Christine Rauch
- Department of Theoretical Chemistry, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, A-6020, Innsbruck, Austria
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