Distamycin-stabilized Antiparallel-Parallel Combination (APC) DNA
Anna K. Shchyolkina1, Lyudmila E. Minchenkova1, Elvira E. Minyat1, Yelena
B. Khomyakova1, Valery I. Ivanov1,
Reinhard Klement2 and Thomas M. Jovin2*
1Engelhardt Institute of Molecular Biology, Russian
Academy of Science, 117984 Moscow, Russia,
2Dep't of Molecular Biology, Max Planck Institute
for Biophysical Chemistry, D-37070 Göttingen, FRG
*Author to whom correspondence should be addressed. Phone: +49-551-2011381;
Fax: +49-551-2011467; E-mail: tjovin@mpc186.mpibpc.gwdg.de.
Abstract
The formation of Antiparallel-Parallel-Combination (APC) DNA, a liner duplex with a segment of parallel-stranded (ps) helix flanked by conventional B-DNA, was tested with a number of synthetic oligonucleotides. The groove-binding ligand distamycin A (DstA) was used to stabilize the ps segment comprising five A·T base pairs. Two drug molecules bound per APC, one in each of the two equivalent grooves characteristic of ps-DNA. APC-DNA, reference molecules and their complexes with DstA were analysed by several methods: circular dichroism and absorption spectroscopy, thermal denaturation, chemical modification, and molecular modeling. The dye binding stoichiometry differed significantly due to inherent structural differences in the groove geometries of ps-DNA (trans base pairs, similar grooves) and conventional antiparallel-stranded (aps) B-DNA (cis base pairs, distinct major and minor grooves). The data support the existence of APC folding in solution.
Homology Model for the Ligand-Binding Domain of the Human Estrogen Receptor
George J. Maalouf1, Wenrong Xu2, Temple F. Smith1 and Scott
C. Mohr2*
1Boston University, BioMolecular Engineering Research
Center, 36 Cummington Street, Boston, MA 02215
2Boston University, Department of Chemistry,
590 Commonwealth Avenue, Boston, MA 02215
*Author to whom correspondence should be addressed. Phone: (617)-353-2172;
Fax: (617)-353-6466; E-mail: mohr@bu.edu
Abstract
We have modeled the ligand-binding domain (LBD) of the human estrogen receptor protein (hER) by homology to the known crystal structure of the LBD of the a isoform of human retinoate-X receptor (hRX). Alignment of hER with members of the nuclear receptor superfamily defined probable secondary structures which we used to constrain backbone torsion angles and hydrogen bonds. From published studies we identified key interactions between hER and estradiol to use to dock the hormone in its ligand-binding pocket. Since the hRX crystal structure corresponds to the unliganded form of the LBD, we adopted the "mousetrap" mechanism proposed by Renaud et al. to predict the structure of the E2-bound hER. Refinement by molecular dynamics and energy minimization gave a model which matches well the known facts about the estradiol phamacophore. It also provides a possible explanation for how hER discriminates between estradiol and testosterone.
Three Dimensional Structure of the Soybean Agglutinin-Gal/GalNAc Complexes by Homology Modeling
V.S.R. Rao, King Lam and Pradman K. Qasba*
Structural Glycobiology Section, Laboratory of Experimental and Computational
Biology, National Cancer Institute, NCI-FCRDC, Frederick, Maryland 21702
*Author to whom correspondence should be addressed. Phone: 301-846 1933;
Fax: 301-846 7149; E-mail: qasba@helix.nih.gov.
Abstract
Complexes of soybean agglutinin (SBA) with galactose (Gal) and N-acetyl galactosamine (GalNAc) have been modeled based on its homology to erythrina corallodendron (EcorL) lectin. The three dimensional structure of SBA-Gal modeled with homology techniques agrees well with SBA-(beta-LacNAc)2Gal-R complex determined by X-ray crystallographic techniques at the beta- sheet regions and the regions where Ca2+ and Mn2+ ions bind. However, significant deviations have been observed between the modeled and the X-ray structures, particularly at the loop regions where the polypeptide chain could not be unequivocally traced in the X-ray structure. The hydrogen bonding scheme, predicted from the homology model, shows that the invariant residues i.e. Asp, Gly, Asn, and aromatic residues (Phe) found in all other legume lectins, bind Gal, slightly in a different way than reported in X-ray structure of SBA-pentasaccharide complex. The higher binding affinity of GalNAc over Gal to SBA is due to additional hydrophobic interactions with Tyr107 rather than a hydrogen bond between N-acetamide group of the sugar and the side chain of Asp88 as suggested from X-ray crystal structure studies. Our modeling also suggest that the variation in the length of the loop D observed among galactose binding legume lectins may not have any effect on the binding of sugar at the monosaccharide specific site of the lectins.
Structure and Dynamics of Elastin Building Blocks. Boc-LG-OEt, Boc-VG-OEt, Boc-VGG-OH.
M. Martino1, A. Bavoso1,
M. Saviano2, B. Di Blasio2,3
and A. M. Tamburro1*
1Department of Chemistry, University of Basilicata,
Potenza, Italy
2CNR Biocrystallography Center, Department of
Chemistry, University of Naples, "Federico II", Naples, Italy
3Department of Environmental Science,II University
of Naples,Caserta, Italy
*Author to whom correspondence should be addressed. Phone: ++39-971-470727;
Fax: ++39-971470718; E-mail: Tamburro@unibas.it
Abstract
Short di- and tripeptides such as Boc-LG-OEt, Boc-VG-OEt and Boc-VGG-OH, corresponding to abundant repetitive sequences in elastin, have been extensively studied both in solid state, by X-ray diffraction, and in solution by circular dicroism and nuclear magnetic resonance. Furthermore, theoretical procedures such as simulated annealing and molecular dynamics were also performed on these peptides.
In general, the results indicate that no one single structure (be folded or extended) could be representative for these sequences in the protein, but rather that a multiplicity of interconverting conformers, ranging from folded to extended structures, should be considered. In any case, these structures, e.g. beta-turns, polyglycine II and beta-conformations, are those previously suggested to participate to conformational equilibria of elastin.
Variability Analysis of HIV-1 gp120 V3 Region: IV. Distribution Functions for Intra- and Inter-Subtype Amino Acid Hamming Distances.
Michael Yu. Shchelkanov1,2, Nicole S.
Starikov1,2, Ilya V. Yaroslavtsev3,
Philip O. Tsvetkov4, Alex N. Yudin1,2, Maxim V. Denisov1, Alexander
A. Slavsky1,2, Alexander A. Vedenov1,5 and Edward V. Karamov2,6*
1Moscow Institute of Physics and Technology, Faculty
of Physicochemical Biology, Department of Molecular Biophysics, Dolgoprudny,
Moscow region, 141700 Russia
2D. I. Ivanovsky Institute ofVirology, Immunochemistry
Group, Gamaley 16, Moscow, 123098, Russia
3Moscow Aviation Institute, Faculty of Mathematics,
Department of Mathematical Cybernetics, Moscow, 115098 Russia
4Institute of Molecular Biology, Moscow, 117989
Russia
5Russian Scientific Center Kurchatov Institute,
Kurchatov s., Moscow, 123182 Russia
6Moscow State University, Institute of Applied
Research, Laboratory of Virology, Lenin's Hills, Moscow, 119899, Russia
*Author to whom correspondence should be addressed. Phone: 7 095 190 3048;
Fax: 7 095 190 2867; E-mail: karamov@invir.msk.su
Abstract
Distribution functions for intra- and inter- HIV-1 V3-loop subtypes amino acid Hamming distances were calculated (850 V3-loop sequences from the Los Alamos HIV-1 Database (1996) were used). These functions have pronounced bell-like shape. Such shapes of the histograms for HIV-1 V3 intra- and inter-subtype distriutions are discussed to confirm the applicability of different hierarchical cluster procedures (see ref. 17) for HIV-1 V3 classification. Two-mode distribution for the subtype E could sertificate that this subtype includes two thinner taxons.
One-parameter Discrete Model of the Genetic Diversity
Michael Yu. Shchelkanov1,2, Lev A. Soinov1, Vadim V. Zalunin1, Dmitrii
A. Gumennyi1, Alex N. Yudin1,2,
Andrei A. Natan1, Victor B. Kireev1 and Edward V. Karamov2,3*
1Moscow Institute of Physicsand Technology, Faculty
of Physicochemical Biology, Department of Molecular Biophysics, Dolgoprudny,
Moscow region, 141700 Russia
2D. I. Ivanovsky Institute ofVirology, Immunochemistry
Group, Gamaley 16, Moscow, 123098 Russia
3Moscow State University, Institute of Applied
Research, Laboratory of Virology, Lenin's Hills, Moscow, 119899 Russia
*Author to whom correspondence should be addressed. Phone: 7 095 190 3048;
Fax: 7 095 190 2867; E-mail: karamov@invir.msk.su
Abstract
One-parameter discrete model estimating genetic distance between precursor
and descendant nucleotide sequences after several steps of substitution
acts is developed. This model based on the previously introduced symbol
sequences enumeration procedure (M.Y. Shchelkanov, A.N. Yudin, A.V. Antonov,
N.S. Starikov, A.A. Vedenov, E.V. Karamov, J. Biomol. Struct. Dyn. 15,
231-241 (1997)) differs from Jukes-Cantor and Kimura models by the absence
of the assumptions usual for continuous Markov's processes. Formula obtained
with the help of our model are more preferable since they take into account
multiple repetition substitution ability and they are correct in the entire
admissible range of parameters.
Effect of Selective Substitution of 5-Bromocytosine on Conformation of DNA Triple Helices
Maozi Liu1, Linjing Yang1,
Wenli Deng1, Ming Su1,
Chen Wang1, Shuu-Bin Lin2,
Lou-sing Kan2* and Chunli Bai1*
1Institute of Chemistry, Chinese Academy of Sciences,
Beijing 100080, China
2Institude of Chemistry, Academia Sinica, Taipei,
China
*Authors to whom correspondence should be addressed.
Bai- Phone: 86-010-62568158; Fax: 86-010-62557908; E-mail: clbai@infoc3.icas.ac.cn
Kan- Phone: 886-2-788-1184; Fax: 886-2-783-1237; E-mail: lskan@chem.sinica.edu.tw.
Abstract
Three triplex DNAs containing 5-bromocytosine[BrC]
were studied by vibrational spectroscopy and molecular modelling. Firstly,
three oligodeoxypyrimidines of 5'-(TC)3-T4-(BrCT)3 [CBrC], 5'-(TBrC)3-T4-(CT)3
[BrCC] and 5'-(TBrC)3-T4-(BrCT)3 [BrCBrC]
were synthesized and then reacted with an oligodeoxypurine of 5'-(AG)3 at pH=4.5 in phosphate buffer respectively to form three
comparative hairpin triplex named CY,YC and YY. The results of FT-Raman
and IR revealed that YY is almost in A-like form, CY and YC are combinations
of A-like form and B-like form, but A-form dominates in CY while B-form
is equivalent as A-form in YC. The result is consistent with the theoretical
analysis.
The Intrinsic Curvature
of a 51 bp K-DNA Fragment of Leishmania tarentolae: A Molecular Model
Osmar Norberto De SouzaÝ and Julia
M. Goodfellow*
Department of Crystallography, Birkbeck College, University of London, Malet
Street, London WC1E 7HX
ÝPresent address: Environmental Molecular
Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA
99352 USA
Phone: (509) 375-3909; Fax: (509) 375-6631; E-mail: mg390@saudade.pnl.gov
*Author to whom correspondence should be addressed. Phone: 171-631-6833;
Fax: 171-631-6803; E-mail: j.goodfellow@mail.cryst.bbk.ac.uk
Abstract
DNA intrinsic structure and curvature is a subject of debate because of the importance of these attributes in processes such as DNA packaging, transcription, and gene regulation. X-ray crystallography of DNA single crystals has provided a wealth of information about the local, short range conformational features of DNA. On the other hand, gel electrophoresis analysis of DNA has not only uncovered the macroscopic curvature of DNA but it also provides most of the available data on DNA intrinsic curvature. However, gel electrophoresis can not identify features of DNA structure at the nucleotide or atomic level. In order to address the problem of DNA intrinsic curvature in an attempt to bridge the gap between X-ray crystallography and gel electrophoresis, we use the computational method of molecular dynamics (MD). In this study, we report the results of 2.0 ns MD simulations on a 51 bp fragment of the K-DNA of Leishmania tarentolae containing several A-tracts. The K-DNA double helix is very stable and remains in an intermediate state between the canonical A and B forms of the duplex. The magnitude of global curvature (75°) agrees well with the experimental estimate (72°) available. Analysis of local (every base triplet) and sublocal (every helix turn) curvature shows that the 51 bp K-DNA fragment has curvature features also present in the Wedge, Junction and Calladine's models of DNA intrinsic curvature. We further characterize the flexibility of individual nucleotides in the molecule and find the sugar flexibility within the A-tracts to be strongly correlated with the pattern of A-tract cleavage by the hydroxyl radical. Differential curvature and flexibility at the 5' and 3' junctions between A-tracts and general-sequence DNA are found to modulate the global curvature of the K-DNA fragment.
Conformational Study of DNA-RNA Duplexes Containing MMI Substituted Phosphodiester Linkages by FTIR Spectroscopy
Hervé Gousset1, Jean Liquier1, Eliane Taillandier1*,
Yogesh S. Sanghvi2 and Didier Peoc´h2
1Laboratoire de Spectroscopie Biomoléculaire, URA CNRS
1430, UFR de Médecine, 74 rue Marcel Cachin, 93017 Bobigny Cedex,
France
2Medicinal Chemistry Department, ISIS Pharmaceuticals,
2292 Faraday Avenue, Carlsbad, California 92008, USA
*Author to whom correspondence should be addressed. Phone: 33 1 48 38 76
90; Fax: 33 1 48 37 74 43; E-mail: etail@tintin.univ-paris13.fr
Abstract
Six methylene(methylimino) (MMI, Bhat et al. J. Org. Chem., 61, 8186, 1996) linked oligonucleotides a-f (* = MMI linkage; 5'-GCGT*TT*TT*TT*TT*TGCG-3') containing various combinations of 2´-O-methyl and 2´-fluoro substituent were synthesized as a model to study the global conformational change upon hybridization to the complement RNA. Fourier transform infrared (FTIR) spectroscopic technique has been used to study and compare the influence of these modifications on the solution conformation of 2´-modified MMI DNA·RNA duplexes. FTIR analysis of the single-stranded RNA (5'-CGCAAAAAAAAAACGC-3') and the modified oligonucleotides a-f showed that all sugar residues adopted a C3'-endo conformation (North-type). Stable duplexes were formed when oligonucleotides a-f were hybridized to the complement RNA. These duplexes retained the original C3'-endo conformation for all sugar residues, hallmark of an A-form of duplex. We postulate that the observed preorganization of the sugar residues and oligonucleotides containing 2'-modified MMI modifications may play an important role in both improving the recognition of RNA target and enhancing the stability of duplex formation with RNA.
Nucleosome Units and Hidden
Periodicities in DNA Sequences
V. R. Chechetkin* and V. V. Lobzin
Troitsk Institute of Innovation and Thermonuclear Investigations (TRINITI),
Theoretical Department of Division for Perspective Investigations, 142092,
Troitsk, Moscow Region, Russia
*Author to whom correspondence should be addressed. E-mailc/o: lobzin@top.izmiran.troitsk.ru
Abstract
The relationship between the hidden periodicities in DNA sequences and the
nucleosome units is investigated. It is shown that in the vicinity of lengths
of about 200 bases there are statistically significant periodicities which
remain approximately universal for exon-intron sequences both in the different
genes and the different eukaryotic species. The additional analysis displays,
nevertheless, that these approximately coincident universal periodicities
can be generated by a variety of mechanisms. The relevance of the features
observed to the structure of chromatin is discussed.
Circular Superhelical DNA Complexes with Synthetic Oligopeptide: Unusual Compact Structures and Influence of Bent Sequences on the Results of Compaction
Larissa P. Martinkina1*, Alexander A.
Kolesnikov2, Sergey. A. Streltsov1,
Vyacheslav Yu. Yurchenko2 and Yuri Yu.Vengerov1
1Engelhardt Institute of Molecular Biology, Russian Academy
of Sciences,Vavilov str., 32, 117984, Moscow, Russia
2Department of Molecular Biology, Lomonosov
Moscow State University, Vorobyevy gory, 119899, Moscow, Russia
*Author to whom correspondence should be addressed. Phone: 007/095/135-41-00;
Fax: 007/095/135-14-05; E-mail: martin@imb.ac.ru
Abstract
The organization of synthetic oligopeptide trivaline (1) complexes with four types of circular superhelical DNA preparations was studied by electron microscopy. The DNA molecules in the preparations investigated had different sizes ranging from 2.9 kb to 21.0 kb. Two plasmids contained bent DNA sequences from minicircles of kinetoplast DNA of Leishmania gymnodactili and Trypanosoma boissoni.
The main structures in all preparations observed were circular compact particles which coincide in their appearance and compaction coefficient (3,5-3,7) with triple rings described earlier. But along with triple rings the new types of compact structures were observed having the shape of a ring with attached rod or the shape of two compact rings attached to each other by a region of compact fiber. The latter structures could be observed in significant quantities in case of DNA preparations longer than 10 kb. The conclusions can be made that due to TVP stimulated compaction of circular DNA molecules compact fibers containing both two or three DNA duplexes arranged side by side can be formed. It is shown that presence of bent DNA sequences stimulates the formation of structures containing more than one triple ring. It demonstrates the possibility of the primary DNA structure influence on the compaction process in case of the circular molecules. The new ways of circular DNA folding described can be of importance for understanding of DNA organization in different cell structures.
A Fluorescence Spectroscopic and Molecular Dynamics Study of bis-ANS/Protein Interaction
Asim Bothra1, Anusree Bhattacharyya1, Chaitali Mukhopadhyay2,
Kankan Bhattacharyya3 and Siddhartha Roy1*
1Department of Biophysics,
2Distributed Information Centre, Bose Institute,
P 1/12 C.I.T. Scheme VII M, Calcutta 700 054, India
3Department of Physical Chemistry, Indian Association
for the Cultivation of Science, Raja Subodh Mullick Road, Calcutta 700 032,
India
*Author to whom correspondence should be addressed. Fax: 91-33-334-3886;
E-mail: siddharth@boseinst.ernet.in
Abstract
Despite emergence of bis-ANS as a major fluorescence probe of proteins structure, conformational and spectroscopic properties of protein/bis-ANS complexes remains largely unexplored. We have shown that fluorescence polarization of both ANS and bis-ANS is excitation wavelength dependent and this is a property of all protein-ANS/bis-ANS complexes studied. Bis-ANS excitation maximum is always more red shifted than the corresponding ANS complex. Even when corrected for the red shift, the bis-ANS complexes in some, but not all, cases show only a little lowering of polarization, suggesting modest additional depolarization in bis-ANS compared to ANS.
Calculation of energy migration rate between the two rings suggests that energy migration rate should be high at all values of the naphthyl-naphthyl dihedral angle. Although, Molecular mechanics and dynamics calculations show that the lowest energy conformation of bis-ANS is when the two naphthalene rings are roughly perpendicular to each other, due to rapid energy migration this conformation should lead to dramatic lowering of emission anisotropy, unlike what is observed. Salt and temperature dependence of bis-ANS/protein interaction suggests little ionic interaction and pre-dominant interaction through hydrophobic aromatic rings. We conclude that bis-ANS binds to proteins through interaction with the aromatic rings and with two rings nearly parallel to each other.
A Study of Metalloporphyrin-polynucleotide Interactions by Microcalorimetry and Circular Dichroism
G. Wheeler1*, P. Miskovsky2,
D. Jancura2 and L. Chinsky1
1LPBC, Université Paris VI, case 138, 4 Place Jussieu,
Cedex 05, 75252 Paris, France
2Division of Biophysics, Safarik University,
Jesenna 5, 041 54 Kosice, Slovakia
*Author to whom correspondence should be addressed. Phone: 01-44-27-75-47;
Fax: 01-44-27-75-60; E-mail: <chinsky@lpbc.jussieu.fr>
Abstract
In this paper we examine the interactions of Calf Thymus DNA and the model polynucleotides poly(dA).poly(dT), poly(dAdT)2 and poly(dG.dC)2 with a group of metalloporphyrins derived from the freebase porphyrin tetrakis(4-N-methylpyridyl)porphine, H2(TMpy-P4), by means of ultraviolet absorption spectroscopy, circular dichroism spectroscopy and microcalorimetry. We have studied the interactions of the copper, cobalt, nickel and zinc derivatives of H2(TMpy-P4) in addition to the free base porphyrin itself. We have found strong evidence for an external self-stacking interaction of the Cu(TMpy-P4) and Zn(TMpy-P4) derivatives with poly(dA).poly(dT) and poly(dAdT)2 even at low concentrations of porphyrin, and all of the porphyrin derivatives studied appear to display such a self-stacking in interaction with poly(dA.dT)2 at sufficiently high ratios of porphyrin to polynucleotide.
A Molecular Dynamics Computer Simulation Study of Nucleotide Analogues. Comparison of the Hydration Pattern of Dithymidine Phosphate with those of the Dithymidine Methylphosphonate Diastereomers
Katarzyna Kulinska1*, Tadeusz Kulinski1, Jacek Stawinski2* and
Aatto Laaksonen3
1Inst. of Bioorganic Chemistry,Polish Academy of Sciences,
Noskowskiego 12/14, 61-704 Poznan, Poland
2Dep't. of Organic Chemistry, Arrhenius Laboratory,
Stockholm University, S-106 91 Stockholm, Sweden
3Dep't. of Physical Chemistry, Arrhenius Laboratory,
Stockholm University, S-106 91 Stockholm, Sweden
*Authors to whom correspondence should be addressed.
Stawinski- Phone: +46 8 16 24 85; Fax: +46 8 15 49 08; E-mail: js@lab12.organ.su.se
Kulinska- Phone: +46 61 852 8503; E-mail: kasiek@ibch.poznan.pl
Abstract
The hydration pattern of thymidyl(3'>5') thymidine 1 and those of RP and SP diastereomers of the corresponding methylphosphonate analogue 2, have been studied using Molecular Dynamics (MD) computer simulation. It was found that the methylphosphonate modification leads to significant changes in the coordination of water molecules around the internucleotidic linkage and these, in turn, affect the hydration pattern of other parts of the molecule. The most notable differences between RP and SP diastereomers 2a and 2b were found to occur at the deoxyribose moieties of the nucleosid-5'-yl units.
Molecular Dynamics Simulation of Colchicinoids
Asim K. Bothra1, Siddhartha Roy1, Bhabatarak Bhattacharyya2
and Chaitali Mukhopadhyay*3,4
1Department of Biophysics,
2Department of Biochemistry and
3Distributed Information Centre, Bose Institute,
Centenary Building, Calcutta 700054, India
4Present Address:Department of Chemistry,University
of Calcutta,92, A.P.C. Road, Calcutta 700009, India
*Author to whom correspondence should be addressed. Phone: 091-33-334-6626;
Fax: 011-33-334-3886; E-mail: chaitali@boseinst.ernet.in
Abstract
Colchicine, a tricyclic alkaloid, has a remarkable range of biological activities. It binds with tubulin and prevents the formation of microtubules. This compound consists of a six membered aromatic ring (A ring), a seven membered troponoid ring (C ring) and another seven membered aliphatic ring (B ring). Using molecular mechanics and molecular dynamics simulations as tools, conformational analysis of colchicine and its several important analogs were done. Molecular mechanics studies show that conformational space of these molecules have one low energy region. Taking the low energy minima as the starting conformation, molecular dynamics simulation for 100 pico seconds is done for each of the analogs and molecular dynamics simulation in solution is done for three representative compounds colchicine,isocolchicine and A-C compound. Internal coordinate trajectories show that the value of the dihedral angle C9-C7-C1-C14 (phi), (C7-C1 bond connects the A and C ring), is within 40° to 50° for all the compounds with fluctuations less than 15°. These calculations indicate that there is an overall similarity in the dynamically averaged structure of all the drugs. The A ring and B ring of the compounds are more or less rigid. The C ring is somewhat flexible, the average conformation and motional properties show overall similarity. The potential energy curve and dynamics behaviour of colchicine and isocolchicine suggests that the difference in binding property of colchine and isocolchicine may originate from the positional difference of carbonyl oxygen and methoxy group of C ring, which is the only difference in the structures of the two compounds and this has no effect on the motional property and average conformations of these two compounds. From our study it is proposed that the movements occuring at various positions of the drug molecules are significantly correlated. It is suggested that such correlated motion may play an important role in the biological property of these compounds.