Rana C. Morris, Kenneth G. Brown and Mark S. Elliott*
Department of Biochemistry and Chemistry,
Old Dominion University,
Norfolk, VA 23529
*Phone: (757) 683-4082; Fax: (757) 683-4628; E-mail: melliott@odu.edu
Abstract
Computational modeling was performed to determine the potential function
of the queuosine modification of tRNA found in wobble position 34 of tRNAasp, tRNAasn, tRNAhis,
and tRNAtyr. Using the crystal structure of tRNAasp
and a tRNA-tRNA-mRNA complex model, we show that the queuosine modification
serves as a structurally restrictive base for tRNA anticodon loop flexibility.
An extended intraresidue and intramolecular hydrogen bonding network is
established by queuosine. The quaternary amine of the 7-aminomethyl side
chain hydrogen bonds with the base's carbonyl oxygen. This positions the
dihydroxycyclopentenediol ring of queuosine in proper orientation for hydrogen
bonding with the backbone of the neighboring uridine 33 residue. The interresidue
association stabilizes the formation of a cross-loop hydrogen bond between
the uridine 33 base and the phosphoribosyl backbone of the cytosine at position
36. Additional interactions between RNAs in the translation complex were
studied with regard to potential codon context and codon bias effects. Neither
steric nor electrostatic interaction occurs between aminoacyl- and peptidyl-site
tRNA anticodon loops that are modified with queuosine. However, there is
a difference in the strength of anticodon/codon associations (codon bias)
based on the presence or lack of queuosine in the wobble position of the
tRNA. Unmodified (guanosine-containing) tRNAasp forms a very stable association
with cytosine (GAC), but is much less stable in complex with a uridine-containing
codon (GAU). Queuosine-modified tRNAasp exhibits no
bias for either of cognate codons GAC or GAU and demonstrates a lower binding
energy similar to the wobble pairing of guanosine-containing tRNA with a
GAU codon. This is proposed to be due to the inflexibility of the queuosine-modified
anticodon loop to accommodate proper positioning for optimal Watson-Crick
type associations. A preliminary survey of codon usage patterns in oncodevelopmental
versus housekeeping gene transcripts suggests a significant difference in
bias for the queuosine-associated codons. Therefore, the queuosine modification
may have the potential to influence cellular growth and differentiation
by codon bias-based regulation of protein synthesis for discrete mRNA transcripts.
Youri Timsit1*, Michal Shatzky-Schwartz2 and Zippora Shakked2
1Institut de Biologie Physico-Chimique CNRS,
13, rue Pierre et Marie Curie
Paris 75005, France
2Department of Structural Biology,
Weizmann Institute of Science
Rehovot 76100 Israel
*Phone: 01 43 25 26 09; Fax: 01 43 29 56 45; E-mail: timsit@ibpc.fr
Abstract
The close approach of DNA segments participates in many biological functions including DNA condensation and DNA processing. Previous crystallographic studies have shown that B-DNA self-fitting by mutual groove-backbone interaction produces right-handed DNA crossovers. These structures have opened new perspectives on the role of close DNA-DNA interactions in the architecture and activity the DNA molecule. In the present study, the analysis of the crystal packing of two B-DNA decamer duplexes d(CCIIICCCGG) and d(CCGCCGGCGG) reveals the existence of new modes of DNA crossing. Symmetric left-handed crossovers are produced by mutual fitting of DNA grooves at the crossing point. New sequence patterns contribute to stabilize longitudinal fitting of the sugar-phosphate backbone into the major groove. In addition, the close approach of DNA segments greatly influences the DNA conformation in a sequence dependent manner. This study provides new insights into the role of DNA sequence and structure in DNA-DNA recognition. In providing detailed molecular views of DNA crossovers of opposite chirality, this study can also help to elucidate the role of symmetry and chirality in the recognition of complex DNA structures by protein dimers or tetramers, such as topoisomerase II and recombinase enzymes. These results are discussed in the context of the possible relationships between DNA condensation and DNA processing.
Nina Pastor1,2, Alexander D. MacKerell
Jr.3 and Harel Weinstein2*
1Facultad de Ciencias,
Universidad Autónoma
del Estado de Morelos,
Av. Universidad 1001,
62120 Cuernavaca,
Morelos, México
2Department of Physiology
and Biophysics, Box 1218
Mount Sinai School of Medicine,
New York, NY 10029, USA
3School of Pharmacy,
University of Maryland,
20 North Pine Street,
Baltimore, MD 21201, USA
*Phone: 212-241-7018; Fax: 212-860-3369; E-mail: hweinstein@inka.mssm.edu
ÝThis article is dedicated to David Beveridge
on the occasion of his 60th birthday.
Abstract
The sequence dependent conformation, flexibility and hydration properties of DNA molecules constitute selectivity determinants in the formation of protein-DNA complexes. TATA boxes in which AT basepairs (bp) have been substituted by IC bp (TITI box) allow for probing these selectivity determinants for the complexation with the TATA box-binding protein (TBP) with different sequences but identical chemical surfaces. The reference promoter Adenovirus 2 Major Late Promoter (mlp) is formed by the apposition of two sequences with very different dynamic properties: an alternating TATA sequence and an A-tract. For a comparative study, we carried out molecular dynamics simulations of two DNA oligomers, one containing the mlp sequence (2 ns), and the other an analog where AT basepairs were substituted by IC basepairs (1 ns). The simulations, carried out with explicit solvent and counterions, yield straight purine tracts, the A-tract being stiffer than the I-tract, an alternating structure for the YRYR tracts, and hydration patterns that differ between the purine tracts and the alternating sequence tracts. A detailed analysis of the proposed interactions responsible for the stiffness of the purine tracts indicates that the stacking between the bases bears the strongest correlation to stiffness. The hydration properties of the minor groove in the two oligomers are distinctly different. Such differences are likely to be responsible for the stronger binding of TBP to mlp over the inosine-substituted variant. The calculations were made possible by the development, described here, of a new set of forcefield parameters for inosine that complement the published CHARMM all-hydrogen nucleic acid parametrization.
David W. Ussery1*, Christopher F. Higgins2 and Alexander Bolshoy1
1Centre for Biological Sequence Analysis, Department of Biotechnology,
The Technical University of Denmark, Building 208,
DK-2800 Lyngby, Denmark
2Nuffield Department of
Clinical Biochemistry and
Imperial Cancer Research Fund Laboratories,
Institute of Molecular Medicine,
University of Oxford,
John Radcliffe Hospital,
Oxford OX3 9DU, UK
*Phone: (+45) 4525 2488; Fax: (+45) 4593 1585; E-mail: Dave@cbs.dtu.dk
Abstract
DNA curvature plays an important role in many biological processes. To study environmental influences on DNA curvature we compared the anomalous migration on polyacrylamide gels of ligation ladders of 11 specifically-designed oligonucleotides. At low temperatures (25°C and below) most of the sequences exhibited a degree of anomalous migration. Increased temperature had a significant effect on the anomalous migration (curvature) of some sequences but limited effects on others; at 50°C only 1 sequence migrated anomalously. Mg2+ had a strong influence on the migration of certain sequences, whilst spermine enhanced the anomalous migration of a different set of sequences. Sequences with a GGC motif exhibited greater curvature than predicted by the presently-used angles for the nearest-neighbour wedge model and are especially sensitive to Mg2+. The data have implications for models for DNA curvature and for environmentally-sensitive DNA conformations in the regulation of gene expression.
O. N. Ozoline1*, A. A. Deev2
and E. N. Trifonov3
1Institute of Cell Biophysics,
Russian Academy of Sciences,
Pushchino,
Moscow Region 142292, Russia
2Institute of Theoretical and Experimental Biophysics,
Russian Academy of Sciences,
Pushchino,
Moscow Region 142292, Russia
3Department of Structural Biology,
The Weizmann Institute of Science,
Rehovot, 76100, Israel
*Phone: 0967-739-140; Fax: 7-0967-790509; E-mail: ozoline@venus.iteb.serpukhov.su
Abstract
The distribution of deformable base-pair steps in the structure of bacterial promoters is analyzed with respect to their possible structural and functional role. A regular positioning of TA and TG stacks is detected with the best fit period 5.6 bp. This value is interpreted as a half of the sequence period 11.2 bp, somewhat higher than the structural helical repeat of B-DNA (10.55 bp). The difference, +0.65 bp, suggests a sequence-dependent helical writhe of the promoter DNA - a right-handed superhelix. Apparently, to favour rotational setting of DNA on the surface of RNA polymerase the flexible steps deformable largely towards the grooves, follow the half-period spacing. Such rotational setting is consistent with the DNase I footprinting data. Periodical distribution of deformable base-pair stacks shows negative correlation with the presence of -35 canonical hexamer, suggesting the functional significance of this novel element for promoter recognition. The RNA polymerase - DNA recognition is discussed as interaction of distributional type that involves many elements of different nature which are in partially compensatory relations.
Xiang-Jun Lu, Marla S. Babcock and Wilma K. Olson*
Department of Chemistry,
Rutgers, the State University of New Jersey,
Wright-Rieman Laboratories,
610 Taylor Road,
Piscataway, NJ 08854-8087
*Author to whom correspondence should be addressed. Phone: (732) 445-3993;
Fax: (732) 445-5958; E-mail: olson@rutchem.rutgers.edu
ÝThis article is dedicated to David Beveridge
on the occasion of his 60th birthday.
Abstract
We outline the mathematical distinctions among seven of the most popular computer programs currently used to analyze the spatial arrangements of bases and base pairs in nucleic acid helical structures. The schemes fall into three basic categories on the basis of their definitions of rotational parameters: matrix-based, projection-based, and combined matrix- and projection-based. The approaches also define and construct base and base-pair coordinate frames in a variety of ways. Despite these mathematical distinctions, the computed parameters from some programs are strongly correlated and directly comparable. By contrast, other programs which use identical methodologies sometimes yield very different results. The choice of reference frame rather than the mathematical formulation has the greater effect on calculated parameters. Any factor which influences the reference frame, such as fitting or not fitting standard bases to the experimentally derived coordinates, will have a noticeable effect on both complementary base pair and dimer step parameters.
Thomas E. Cheatham, III1, Piotr Cieplak2 and Peter A. Kollman3*
1Laboratory of Biophysical Chemistry,
National Heart, Lung, and Blood Institute, 12A-2041,
National Institutes of Health,
9000 Rockville Pike,
Bethesda, MD 20892-5626
2Department of Chemistry,
University of Warsaw,
Pasteura 1,
02-093 Warsaw, Poland
3Department of Pharmaceutical Chemistry
University of California,
San Francisco, CA 94143-0446
*Phone: 415-476-4637, Fax: 415-476-0688; E-mail: pak@cgl.ucsf.edu
ÝThis article is dedicated to David Beveridge on the occasion of
his 60th birthday.
Abstract
We have examined some subtle parameter modifications to the Cornell et al. force field, which has proven quite successful in reproducing nucleic acid properties, but whose C2'-endo sugar pucker phase and helical repeat for B DNA appear to be somewhat underestimated. Encouragingly, the addition of a single V2 term involving the atoms C(sp3)-O-(sp3)-C(sp3)-N(sp2), which can be nicely rationalized because of the anomeric effect (lone pairs on oxygen are preferentially oriented relative to the electron withdrawing N), brings the sugar pucker phase of C2'-endo sugars to near perfect agreement with ab initio calculations (W near 162º). Secondly, the use of high level ab initio calculations on entire nucleosides (in contrast to smaller model systems necessitated in 1994-95 by computer limitations) lets one improve the c torsional potential for nucleic acids. Finally, the O(sp3)-C(sp3)- C(sp3)-O(sp3) V2 torsional potential has been empirically adjusted to reproduce the ab initio calculated relative energy of C2'-endo and C3'-endo nucleosides. These modifications are tested in molecular dynamics simulations of mononucleosides (to assess sugar pucker percentages) and double helices of DNA and RNA (to assess helical and sequence specific structural properties). In both areas, the modified force field leads to improved agreement with experimental data.
Xue-Guang Sun, En-Hua Cao*, Yu-Jian He and Jing-Fen Qin
Institute of Biophysics,
Chinese Academy of Sciences,
15 Datun Road, Chaoyang District,
Beijing 100101, China
*Phone: +86-10-64888567; Fax: +86-10-64877837; E-mail: caoeh@sun5.ibp.ac.cn
Abstract
Six different nucleic acid structures including duplex, triplex and quadruplex are formed by oligonucleotides. Their structural properties are studied in detail by four spectroscopic techniques, i.e. CD, UV, NMR and fluorescence. Results are: CD Spectra: The common characteristics is a negative band at 240 nm, and the spectra are different from each other in the range 260-300 nm. Many factors such as chain direction, sugar puckering, orientation of the glycosyl bond, base stacking and sequence can effect their conformation and then show diversity and complexity in the spectra. UV Spectra: The UV spectra of all forms are quite similar, all of them exhibit a sharp positive peak around 210 nm and a broad positive band in the region of 240-280 nm. Although the bands are different in absorbance, the spectra are not characteristic enough to distinguish these forms. In addition, their thermal denaturation is also observed by UV spectrum, different melting curves and points are shown and some thermodynamic information is provided. NMR Spectra: Since the G residues in the six samples all participate in hydrogen bond, the imino proton can not exchange with the solvent freely so as to allow an observable resonance to arise. The resonance number and chemical shift will vary with the change in base-pairing number and mode as well as the whole geometry of its molecule. Fluorescence Spectra: The interaction mechanisms between EB and these structures are different. B type duplex and triplex adopt an intercalative mode in which the efficiency of energy transfer is relatively high and the fluorescence of EB can not be quenched easily. While for the parallel duplex, outside binding is predominant in which energy transfer can hardly happen and most of its fluorescence can be quenched. As for the quadruplex, groove binding is possible, so the efficiency of energy transfer is higher than that in outside binding, but lower than that in intercalative binding, and fluorescence is quenched partly.
Rachid C. MarounÝ*
Unité d'Immunologie Structurale,
Institut Pasteur,
25-28, rue du Dr. Roux,
75724 Paris Cedex 15, France
ÝPresent address: Unité des Venins
*Phone: 33 1 40 61 34 97; Fax: 33 1 40 61 30 57; E-mail: rmaroun@pasteur.fr.
Abstract
The Val99-Gly104 variable region in egg white lysozyme is part of the active site cleft and of the epitope recognized by some monoclonal antibodies. In general, this loop is found in a conformation inflected towards the active site (proximal conformational) such as in free hen lysozyme (HEL). But in a lysozyme such as Japanese quail's (JEL), the loop turns away from the active site cleft (distal conformation).
In order to differentiate sequence effects from crystal packing, we generated and refined loop conformations for the 99-104 variable region in lysozyme, then estimated their relative conformational free energies. Some of the results indicate that (i) the flexibility of the 99-104 segment is much greater for HEL than for JEL sequences when unconstrained by the crystal lattice, (ii) for JEL, only distal structures are favored, while for HEL the states span the zone between proximal and distal regions, and (iii) epitopes elucidated from crystal structures may not always be conserved in solution. For the JEL loop, model building shows that an energy-costly distal to proximal transition appears necessary.
Finally, analysis of available structural data indicates that changes of humidity, temperature and pressure on loop conformation are negligible.
Indrani Dey*
Distributed Information Centre,
Bose Institute,
p1/12, C. I. T. Scheme,
Calcutta-700 054, India
*Phone: 91-33-334-2816, 91-33-334-6626; Fax: 91-33-334-3886; E-mail: idey@boseinst.ernet.in
Abstract
A semi-empirical method for estimation of binding free energy, recently proposed by Aqvist and coworkers, has been effectively tested in several protein-ligand binding cases. We have applied this linear interaction energy method to predict the binding of some N-benzyloxycarbonyl-L-phenyl alanyl-L-alanine ketones with bovine cathepsin B and computed the respective absolute binding constants from averages of molecular dynamics simulations. It is found that the computer simulation results agree well with available experimental data and make it possible to understand better the origin of tight binding and inhibitor specificity of cathepsin B.
V. Kothekar*, Shakti Sahi and M. Srinivasan
Department of Biophysics,
All India Institute of Medical Sciences,
Ansari Nagar, New Delhi-110 029, India
*Fax: 0091-11-6862663, E-mail: kothekar@medinst.ernet.in
Abstract
We have applied computer simulation technique to study interaction of
two anti-inflammatory drugs (NSAIDs) indoprofen and NS398 with cyclooxygenase
(COX-1 and COX-2) enzymes. We have also investigated conformational flexibility
of the two drugs by systematic search and simulated annealing molecular
dynamics (SAMD) methods. Both the drugs were docked in the cyclooxygenase
channel using in house docking program IMF1. The complexes were energy minimised
by molecular mechanics (MM) method. These were heated for 30 picoseconds
(ps), equilibrated for 110 ps at 300K and subjected to 'production simulation'
for 110 ps by molecular dynamics (MD) method using Sanderís module
of AMBER 5.0 package and united atom force field mostly from PARM96.DAT.
Integration was carried out with time step of 0.001 ps, distance dependent
di-electric constant with scaling factor 2.0 for 1-4 interaction and cut-off
distance for non-bonded pair-list equal to 8Å. The non-bonded pair-list
was upgraded after every 20 cycles. The coordinate output from MD trajectories
is analysed using analysis package of AMBER 5.0, MOLMOL, P-CURVES 3.0 and
in house packages: ANALMD, ANALP1. We have observed perturbative changes
in COX-1 and COX-2 structures due to indoprofen and NS398. In case of indoprofen
specific changes between COX-1 and COX-2 were noted in helix D, H6,
S6 and helix H8 in the cyclooxygenase cavity.
In case of NS398 these were in helix B in membrane binding
domain, helix H6, S8 and S10 in
cyclooxygenase cavity and helices H14-H16 in small lobe close
to haem binding region. Implications of these results in enzyme selectivity
by NSAIDs is discussed here.
L.N. Drozdov-Tikhomirov*, G.I. Skurida and A.A. Alexandrov
Institute of Molecular Genetics,
Russian Academy of Sciences,
Kurchatov sq.,
Moscow 123182, Russia
*Phone: (095) 196-02-01; Fax: (095) 196-02-21; E-mail: Drozdov@img.ras.ru
Abstract
A new kinetic model of enzymatic catalysis is proposed, which postulates that enzyme solutions are equilibrium systems of oligomers differing in the number of subunits and in the mode of their assembly. It is suggested that the catalytic and regulatory sites of allosteric enzymes are of composite nature and appear as a result of subunits joining. Two possible joining modes are postulated at each oligomerization step. Catalytic site may arise on oligomer formed only by one of these modes. Effector acts by fastening together components of certain oligomeric form and increases the life time of this form. It leads to a shift of oligomer equilibrium and increases a proportion of effector-binding oligomers. Effectors-activators bind the oligomers carrying composite catalytic sites and effectors-inhibitors bind the oligomers, which do not carry active catalytic sites. Thus, catalytic activity control in such system is explained by effector-induced changes of a catalytic sites number, but not of a catalytic site activity caused by changes of subunit's tertiary structure.
The postulates of the model do not contradict available experimental data and lead to a new type of general rate equation, which allows to describe and understand the specific kinetic behavior of allosteric enzymes as well as Michaelis type enzymes. All known rate equations of allosteric
The equation was tested by modeling the kinetics of human erythrocyte phosphofructokinase. It enabled to reproduce quantitatively the 66 kinetic curves experimentally obtained for this enzyme under different reaction conditions.
Alexander M. Andrianov*
Institute of Bioorganic Chemistry,
Belarus Academy of Sciences,
Kuprevich St., 5/2,
220141 Minsk,
Republic of Belarus
*Phone: 0-375-17-2637271; Fax: 0-375-17-2637132; E-mail: ibochbel@ns.igs.ac.by
Abstract
The model of spatial structure for the principal neutralizing determinant (PND) of the HIV-1 envelope protein gp120 is proposed in terms of two-dimensional nuclear Overhauser effect (NOE) spectroscopy data. To build the model, the NMR-based theoretical conformational analysis of synthetic PND peptides of length 40, 24, and 12 residues is carried out. The modeling of the molecular spatial structures is performed by a new approach to research of conformationally mobile peptides using the algorithms of the restrained molecular mechanics method developed earlier. The following major conclusions are made based on the analysis of the simulated peptide conformations: i) there is not unique PND structure in solution, ii) there are seven different PND structures each of which agrees with the experimental data and stereochemical criteria used in computing its spatial model, iii) the PND is characterized by irregular conformation containing a number of reverse turns, iv) all of the selected conformations are conserved in the Gly-Pro-Gly-Arg-Ala-Phe stretch, the most probable viral immunodominant epitope. These data allow to suppose that binding properties of this site are determined by the structural motif which forms the conformation of a double b-turn and appears common for all hexapeptide structures.
Nicolay Ya. Orlov1,2*, Tatiana G. Orlova1,2, Yana K. Reshetnyak2,
Edward A. Burstein2* and Narimichi Kimura1
1Institute of Theoretical and Experimental Biophysics,
Russian Academy of Sciences,
Pushchino, 142292 Russia
2Department of Molecular Biology,
Tokyo Metropolitan Institute of Gerontology, 35-2,
Sakae-cho, Itabashi-ku,
Tokyo 173, Japan
*Phone: (7)-(0967)-739-398; Fax: (7)-(0967)-79-05-53; E-mail: orlov@fluor.iteb.serpukhov.su;
burstein@fluor.iteb.serpkhov.su
Abstract
Nucleoside diphosphate (NDP) kinases of mammals are hexamers of two sorts of randomly associated highly homologous subunits of 152 residues each and, therefore exist in cell as NDP kinase isoforms. The catalytic properties and three-dimensional structures of the isoforms are very similar. The physiological meaning of the existence of the isoforms in cells remained unclear, but studying recombinant rat NDP kinases a(lpha) and b(eta), each containing only one sort of subunits, we discovered that, in contrast to the isoenzyme b(eta), NDP kinase a(lpha) is able to interact with the complex between bleached rhodopsin and G-protein transducin in retinal rod membranes at lowered pH values (Orlov et al. FEBS Lett. 389, 186-190, 1996). In order to search for possible molecular basis of such differences between these isoenzymes, a detailed comparative study of their intrinsic fluorescence properties in a large range of solvent conditions was performed in this work. The isoenzymes a(lpha) and b(eta) both contain the same three tryptophan (Trp78, 133, 1nd 149) and four tyrosine (Tyr 52, 67, 147, and 151) residues per subunit, but exhibit pronounced differences in their fluorescence properties (both in spectral positions and shape and quantum yield values) and behave differently under pH titration. Whereas NDP kinase a(lpha) undergoes spectral changes in the pH range 5-7 with the mid-point at 6.2, no unequivocal indication of a structural change of NDP kinase b(eta) under pH titration from 9 to 5 was obtained. Since the pH dependencies obtained for fluorescence of isoenzyme a(lpha) resembles the dependence of its binding to the rhodopsin-transducin complex it was suggested that the differences between the NDP kinase isoenzymes a(lpha) and b(eta) in the pH-induced behavior, revealed by the fluorescence spectroscopy, and the differences in their ability to interact with rhodopsin-transducin complex may have the same physical nature, that would be a physico-chemical reason of possible functional dissimilarity of NDP kinase isoforms in cell. An additional analysis of three-dimensional structure of homologous NDP kinases revealed that the source of the differences in fluorescence properties and pH-titration behavior between the isoenzymes a(lpha) and b(eta) may be due to the difference in their global electrostatic charges, rather than to any structural differences between them at neutral pH. The unusually high positive electrostatic potential at he deeply buried active site Tyr52 makes possible that it exists in deprotonated tyrosinate form at neutral and moderately acidic solution. Such a possibility may account for rather unusual fluorescence properties of NDP kinase a(lpha): (i) rather long-wavelength emission of NDP kinase a(lpha) at ca. 340 nm at pH ca. 8 at extremely low accessibility to external quenchers and, possibly, (ii) an unusually high quantum yield value (ca. 0.42).
Robert Casad1Ý* and Tatiana Volkova2
1Department of Biophysical Chemistry,
University of Basel, Biocenter,
70 Klingelbergstrasse,
CH-4056 Basel, Switzerland
2Shemaykin and Ovchinnikov
Institute of Bioorganic Chemistry,
Russian Academy of Science,
16/10 Mikluhko-Maklaya,
117871 Moscow, Russia
ÝCurrent address:
Institute of Crystallography,
Free University of Berlin,
Takustrase 6, 14195 Berlin, Germany
*Currently: Phone: 0049-30-8384588; Fax: 0049-30-8386702; E-mail: yannis@chemie.fu-berlin.de
Abstract
This study reports rate-of-dialysis of an iodinated N-methyl-D-aspartate antagonist drug, [125-I] MK-801, from solutions of lipid vesicles and from proteoliposomes containing purified membrane proteins. A 170 kd protein precipitated from proteoliposomes cross reacts with monoclonal antibodies against cloned NMDA-NR2(A) and NR2(B) subunits. Drug binding in proteoliposomes includes contributions from lipid and from protein, in addition to lipid. A significant change in drug binding was observed in proteoliposomes in response to 10 uM agonist, NMDA. Rate-of-dialysis from agonist-stimulated proteoliposomes was sensitive to perturbation by decreased aqueous ligand concentration in a manner consistent with a lipid-mediated receptor/antagonist equilibrium.
Ju.V. Milchevsky1, B.S. Zhorov2, N.G. Esipova1 and V.G.
Tumanyan1*
1Engelhardt Institute of Molecular Biology,
Russian Academy of Sciences,
Vavilov str. 32,
117984, Moscow, Russia
2Sechenov Institute of Evolutionary Physiology
and Biochemistry,
Russian Academy of Sciences,
Thorez av. 44,
194223, St. Petersburg, Russia
*Phone: 7(095)135 6000; Fax: 7(095)135 1405; E-mail: tuman@imb.imb.ac.ru
Abstract
This paper concerns the conformational variability of collagen as related to the concrete tripeptides (GXY)n constituting its primary structure. The previously elaborated model (V.G.Tumanyan, N.G.Esipova, Biophysics 28, 1021-1025, 1983) with two nets of hydrogen bonds is useful for tripeptides where X is an amino acid. If X is an imino acid, the common one-bonded Rich & Crick model is valid. In this work, compound sequences including tripeptides of different types are considered. Molecular mechanics is used to assess the conformations of the junction regions when a structure with two nets of hydrogen bonds precedes the structure with one net, and vice versa. Thus, all types of sequences typical for natural collagen are covered. It is shown that the combined model representing an alternation of the two-H-bonded model and the one-H-bonded Rich & Crick model is satisfactory stereochemically, and provides more favorable energy in comparison with the continuous one-H-bonded model. Besides, a more favorable hydration of the molecule occures in this case. Some conclusions are made about interchain and intrachain ionic bonds. Thus, it is deduced for the concrete fibrillar protein how a one-dimensional structure determines three-dimensional structure. The macromolecular structure thus suggested is in accord with the experimental data on hydrogen exchange.