From ryszard { *at * } lisa.moldyn.com Mon Nov 24 13:35:14 1997 Received: from worf.moldyn.com for ryszard at.at lisa.moldyn.com by www.ccl.net (8.8.3/950822.1) id MAA05974; Mon, 24 Nov 1997 12:55:13 -0500 (EST) Received: from lisa.moldyn.com by worf.moldyn.com via ESMTP (950413.SGI.8.6.12/950213.SGI.AUTOCF) for < ( ( at ) ) worf.moldyn.com:CHEMISTRY ( ( at ) ) www.ccl.net> id MAA12997; Mon, 24 Nov 1997 12:55:01 -0500 Received: by lisa.moldyn.com (951211.SGI.8.6.12.PATCH1502/940406.SGI.AUTO) id MAA26328; Mon, 24 Nov 1997 12:54:59 -0500 Date: Mon, 24 Nov 1997 12:54:57 -0500 (EST) From: Ryszard Czerminski To: CHEMISTRY (- at -) www.ccl.net Subject: tRNA modelling: summary Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII ---- Original question: Dear All, I am looking for information about tRNA modelling. In particular for MD simulations and parametrization of rare nucleotides (pseudo-uracil etc...) Ryszard Czerminski phone : (617)354-3124 x 13 Moldyn, Inc. fax : (617)491-4522 955 Massachusetts Avenue e-mail: ryszard # - at - # moldyn.com Cambridge MA, 02139-3180 or ryszard "-at-" photon.com SUMMARY: If anybody has information about charges (preferably published) used for rare nucleotides either with amber or charmm ff I would appreciate to hear from you... RC. ---- Thank you to all who responded (in chronological order) Darrell R. Davis Christoph Schneider Thomas Hermann John E. Reissner Kevin J. Mcconnell Pascal Auffinger ---- useful RNA links http://www.imb-jena.de/RNA.html http://www.ibc.wustl.edu/~zucker/ma (does not work ?) http://algodones.unm.edu/~phraber/ma.html (does not work ?) ---- and recent references ---- (biased by my interests and by no means complete) % % tRNA structure and dynamics % <-at-> INCOLLECTION{Auffinger98, AUTHOR = "Pascal Auffinger and Eric Westhof", BOOKTITLE = "Modification and Editing of RNA: The alternation of RNA Structure and Function", chapter = 6, title = "Effects of Pseudouridylation on tRNA Hydration and Dynamics: A Theoretical Approach", PUBLISHER = {Americal Society for Microbiology}, ADDRESS = {Washington, DC 20005}, YEAR = 1998 } -AatT- INCOLLECTION{Auffinger97a, AUTHOR = "Pascal Auffinger and Eric Westhof", BOOKTITLE = "Enclyclopedia of computational chemistry", title = "Molecular Dynamics Simulations of Nucleic Acids", PUBLISHER = {Wiley \& Sons}, ADDRESS = {NY}, YEAR = 1997 } #*at*# ARTICLE{Hermann97, author = "Thomas Hermann and Pascal Auffinger and William G. Scott and Eric Westhof", title = {Evidence for a hydroxide ion bridging two magnesium ions at the active site of the hammerhead ribozyme}, journal = {Nucl. Acid Res.}, year = 1997, volume = 25, number 17, pages = {3421-3427}, abstract = {In the presence of magnesium ions cleavage by the hammerhead ribozyme RNA at a specific residue leads to 2'3'-cyclic phosphate and 5'-OH extremities. In the cleavage reaction an activated ribose 2'-hydroxyl group attacks its attached 3'-phosphate. Molecular dynamics simulations of the crystal structure of the hammerhead ribozyme, obtained after flash- freezing of crystals under conditions where the ribozyme is active, provide evidence that a $\mu$-bridging OH$^-$ ion is located between the two Mg$^{+2}$ ions close to the cleavable phosphate. Constrained simulations show further that a flip from the C3'-endo to the C2'-endo conformation of the ribose at the cleavable phosphate brings the 2'-hydroxyl in proximity to both the attacked phosphorus atom and the $\mu$-bridging OH$^-$ ion. Thus, the simulations lead to a detailed new insight into the mechanism of hammerhead ribozyme cleavage where a $\mu$-hydroxo bridged magnesium cluster, located on the deep groove side, provides an OH$^-$ ion that is able to activate the 2'-hydroxyl nucleophile after a minor conformational change in the RNA.}} -0at0-ARTICLE{Auffinger97b, author = "Pascal Auffinger and Eric Westhof", title = {{RNA} Hydration: Three nanoseconds of multiple molecular dynamics simulations of the solvated {tRNA$^{Asp}$} anticodon hairpin.}, journal = {J. Mol. Biol.}, year = 1997, volume = 269, pages = "326-341", abstract = {The hydration of the tRNA$^{Asp}$ anticodon hairpin was investigated through the analysis of six 500 ps multiple molecular dynamics (MMD) trajectories generated by using the PME method for the treatment of the long-range electrostatic interactions. Although similar in their dynamical characteristics, these six trajectories display different local hydration patterns reflecting the landscape of the ``theoretical'' conformational space being explored. The statistical view gained through the MMD strategy allowed us to characterize the hydration patterns around important RNA structural motifs such as G-U base pair, the anticodon U-turn, and two modified bases: pseudouridine and 1-methylguanine [...] No long-lived hydrogen bond between water and a 2'-hydroxyl has been observed. Water molecules with long-residence times are found bridging adjacent pro-R$_P$ phosphate atoms. The conformation of the pseudouridine is stiffened by a water-mediated base-backbone interaction and the 1-methylguanine is additionally stabilized by long-lived hydration patterns. Such long-lived hydration patterns are essential to ensure the structural integrity of this hairpin motif. Consequently, our simulations confirm the conclusions reached from an analysis of X-ray crystal structures according to which water molecules form an integral part of nucleic acid structure. The fact that the same conclusion is reached from a static and a dynamic point of view suggest that RNA and water together constitute the biologically relevant functional entity}} (- at -) ARTICLE{Auffinger97c, AUTHOR = {Pascal Auffinger and Shirley Louise-May and Eric Westhof}, TITLE = {Hydration of C-H groups in tRNA}, JOURNAL = {Faraday Discuss.}, YEAR = 1997, VOLUME = 103, PAGES = {151-174}, abstract = {MD simulations of the anticodon hairpin of tRNA$^Asp$ and of full tRNA, both in a solvent bath with neutralizing NH$_4^+$ counter ions, have been produced with the particle mesh ewald (PME) method and multiple molecular dynamics (MMD) strategy [...]}} ()at()ARTICLE{Auffinger97d, author = "Pascal Auffinger and Eric Westhof", title = {{RNA} Hydration: Three nanoseconds of multiple molecular dynamics simulations of the solvated {tRNA$^{Asp}$} anticodon hairpin.}, journal = {J. Mol. Biol.}, year = 1997, volume = 274, pages = "54-63", abstract = {MD simulations reveal that, in C$_{3'}$-endo sugar puckers, only three orientations are accessible to the 2'-hydroxyl groups distinctive of RNA molecules: towards (i) the O$_{3'}$, (ii) the O$_{4'}$ of the same sugar, and (iii) the shallow groove base atoms. In the rarer C$_{2'}$-endo sugar puckers, orientations towards the O$_{3'}$ atom of the same sugar are strongly favoured. Surprisingly, in helical regions, the frequently suggested intra-strand O$_{2'}$ - H(n)...O$_{2'}$(n+1) interaction is not found. This observation led to the detection of an axial C-H...O interaction between the C$_{2'}H(n) group and the O$_{4'}$(n+1) atom contributing to the stabilization of RNA helical regions. Subsequent analysis of crystallographic structures of both RNA and A-DNA helices fully supports this finding. Specific hydration patterns are also thought to play a significant role in the stabilization of RNA structures. In the shallow groove of RNA, known as a favorable RNA or protein binding region, three well defined hydration sites are located around the O$_{2'}$ atoms. These hydration sites, occupied by water molecules exchanging with a bulk, constitute after dehydration, anchor points for specific interactions between RNA and nucleic acids, proteins or drugs. Therefore, the fact that the 2'-hydroxyl group is not monopolised by axial stabilization, together with its water like behavior, facilitates complex formation involving RNA helical regions.}} ^at^ ARTICLE{Jia97, author = {Yiwei Jia, Alexander Sytnik, Liangquan Li, Serguei Vladimirov, Barry S. Cooperman, and Robin M. Hochstrasser}, title = {Nonexponential kinetics of a single {tRNA$^{Phe}$} molecule under physiological conditions}, journal = {Proc. Natl. Acad. Sci. USA, Biophysics}, year = 1997, volume = 94, pages = "7932-7936", abstract = {The fluorescence decay functions of individual, specifically labeled tRNAPhe molecules exhibit nonexponential character as a result of conformational dynamics occurring during the measurement on a single molecule. tRNAPhe conformational states that interchange much more slowly are evidenced by the distribution of lifetimes observed for many individual molecules. A structural model for the nonexponential decay indicates that the tRNAPhe-probe adduct fluctuates between two states, one of which provides conditions that quench the probe fluorescence.} } .,at,.MISC{Lahiri97, author = "Ansuman Lahiri and Lennart Nilsson", title = {Molecular dynamics study of the anticodon loop of Yeast tRNAphe}, howpublished = "http://hackberry.chem.niu.edu/ECCC4/articles/article41" year = 1997, month = November, abstract = {Molecular dynamics simulations of the aqueous solution of Yeast tRNAphe anticodon loop with counterions were carried out. We looked at the stability of the system and the simulation protocol by a long simulation (over 1 ns) and a set of shorter simulations (duration 300 ps each) which differed only in the initial velocity assignments. In all the cases, the structure remains close to the starting crystal structure with a 3'-stacked conformation nicely maintained. We have also investigated the dynamics of the anticodon loop interacting with UUU and UUC ribotrinucleotide diphosphates, codons for the amino acid phenylalanine.}, note = {CHARMM22 all atom parameter set + modified parameters for rare nucleotides}} -0at0-ARTICLE{Auffinger96a, author = {P. Auffinger and E. Westhof}, title = {H-bond stability in the {tRNA$^{Asp}$} anticodon hairpin: 3 ns of multiple molecular dynamics simulation}, journal = "Biophys. J.", year = 1996, volume = 71, pages = "940-954", abstract = { Multiple MD trajectories of the solvated and neutralized 17-residue tRNS$^{Asp}$ anticodon hairpin were generated for a total of 3 ns. Explicit treatment of all long-ranged electrostatic interactions by the particle mesh Ewald algorithm, as implemented in the AMBER MD software package, effected a degree of structural stabilization not previously achieved by use of a long 16A solvent interaction truncation scheme. The increased stability of this multiple molecular dynamics set was appropriate for an in-depth analysis of the six 500-ps-long trajectories and allowed the characterization of a number of key structural interactions. The dynamical behavior of the standard Watson-Crick base-pairs, the noncanonical G30-U40 ``wobble'' base pair, and the $\Psi$32-C38 pseudo-baise pair is presented as well as that of two C-H...O hydrogen bonds found to contribute to array of tertiary interactions that stabilize the seven-nucleotide native loop conformation. The least mobile residue in the loop is U33, which forms the U-turn motif and which participates in several hydrogen-bonding interactions, whereas the most mobile residue is the apical residue G34 at the wobble position, a factor undoubtedly important in its biologocal function. The set of multiple molecular dynamics trajectories does not converge on a 500-ps time scale to a unique dynamical model but instead describes an ensemble of structural microstates accessible to the system under the present simulation protocol, which is the result of local structural heterogeneity rather than of global conformational changes.}} <-at-> ARTICLE{Auffinger96b, author = "P. Auffinger and E. Westhof", title = {Molecular dynamics simulations of the anticodon hairpin of tRNA$^{Asp}$: Structuring effects of C-H...O hydrogen bonds and of long-range hydration forces}, journal = JACS, year = 1996, volume = 118, pages = "1181-1189", abstract = {The inclusion of long-range sovent interactions out to 16A in a molecular dynamics study of the anticodon loop of tRNA$^{Asp}$ led to an overall structural stabilization of the RNA hairpin tertiary interactions in a set of six independent fully solvated and neutralized 100ps MD trajectories as compared to a shorter-ranged solvent interaction electrostatic model (8A). The increased structural stabilization allowed for the emegence of non-classical C-H...O hydrogen bonds in the MD trajectories. The presence of the C-H...O hydrogen bonds in the crystal structure was subsequently verified and dynamically characterized and their contribution to the preservation of the tertiary native conformation was assessed [...]} } { *at * } ARTICLE{Louise96, AUTHOR = {Shirley Louise-May and Pascal Auffinger and Eric Westhof}, TITLE = {Calculations of nucleic acid conformations}, JOURNAL = {Curr. Opin. Struct. Biol.}, YEAR = 1996, VOLUME = 6, PAGES = {289-298}, abstract = {The present computational power and sophistication of theoretical approaches to nucleic acid structural investigation are sufficient for the realization of static and dynamic models that correlate accurately with current crystallographic, NMR and solution-probing structural data, and consequently are able to provide valuable insights and predictions for a variety of nucleic acid conformational families. In molecular dynamics simulations, the year 1995 was marked by the foray of fast Ewald methods, an accomplishment resulting from several years' work in the search for an adequate treatment of the electrostatic long-range forces so primordial in nucleis acids behavior. In very large systems, and particularly in the RNA-folding field, techniques originating from artificial intelligence research, like constraint satisfaction programming or genetic algorithms, have established their utility and potential.}} at.at ARTICLE{Westhof96a, author = "E. Westhof et al.", title = {}, journal = Science, year = 1996, volume = 272, pages = "1343", abstract = {} } $#at#$ ARTICLE{Auffinger95, AUTHOR = {P. Auffinger; S. Louise-May; E. Westhof}, TITLE = {Multiple molecular dynamics simulations of the anticodon loop of tRNA$^Asp$ in aqueous solution with counterions}, JOURNAL = JACS, YEAR = 1995, VOLUME = 117, PAGES = {6720-6726}, abstract = {In a systematic search for a stable protocol with which to extend our dynamical investigations, a nanosecond of MD simulations of the solvated anticodon loop of tRNA$^Asp$ consisting of ten unique trajectories was obtained by slight modifications to the starting conditions. These changes produced divergent trajectories which varied widely in structural and dynamical characteristics. However, the properties of these trajectories could not be directly correlated to the slight modifications introduced in the system, and thus, questions were raised regarding the probity of the standard protocol we utilized. Instead of a detailed analysis of the results, the multiple molecular dynamics approach was used as a diagnostic for estimating the reliability of the set of trajectories generated and the extent of relevant biochemical information which cen be extracted from it. We address here issues concerning critical evaluation of molecular dynamics methodology and detection of protocol instabilities. We infer that an ensemble of initial uncorrelated trajectories should be generated in order to investigate the constancy of structural and dynamical properties of the system under study}} .,at,.ARTICLE{Nakamura94, author = {Shugo Nakamura and Junta Doi}, title = {Dynamics of transfer RNAs analyzed by normal mode calculation}, journal = {Nucl. Acids Res.}, year = 1994, volume = 22, number = 3, pages = {514-521}, abstract = {Normal mode calculation is applied to tRNA$^{Phe}$ and tRNA$^{Asp}$, and their structural and vibrational aspects are analyzed. Dihedral angles along the phosphate-riboze backbone ($\alpha, \beta, \gamma, \epsilon, \ksi$) and dihedral angles of glycosyl bonds ($\chi$) are selected as movable parameters. The calculated displacement of each atom agrees with experimental data In modes with frequencies higher then 130cm$^{-1}$, the motions are localized around each stem and the elbow region of the L-shape. On the other hand, collective motions such as bending and twisting of arms are seen in modes with lower frequencies. Hinge axes and bend angles are calculated without prior knowledge. Movements in modes with very low frequencies are combinations of hinge bending motions with various hinge axes and and bend angles. The thermal fluctuations of dihedral angles well reflect the structural changes of transfer RNAs. There are some dihedral angles of nucleotides located around the elbow region of L-shape, which fluctuate about five to six time more than the average value. Nucleotides in the position seem to be influential in the dynamics of the entire structure. The normal mode calculation seems to provide much information for the study of conformational changes of transfer RNAs induced by aminoacyl-tRNA synthetase or codon during molecular recognition}} &$at$& ARTICLE{Nardi94, author = {F. Nardi and W. Doster and B. Tidor and M. Karplus and S. Cusack and J. C. Smith}, title = {Dynamics of tRNA: Experimental Neutron Spectra Compared with Normal Mode Analysis}, journal = {Israel J. Chem.}, year = 1994, volume = 34, pages = {233-238}, abstract = {A comparison is made of experimental inelastic neutron scattering spectra from tRNA with spectra calculated from a normal mode analysis. The experimental data indicate that a dynamic transition occurs with temperature, as is seen in proteins. At low temperatures a broad peak is seen in the dynamic structure factor, due to the lowest frequency collective modes. This peak is centered at ~40cm$^{-1}$, somewhat higher than that observed in small globular proteins. The vibrational frequency distribution calculated from the normal mode analysis rises to a broad maximum at ~50cm$^{-1}$, in general accord with the experiment. However the lowest frequency vibrations in the harmonic model (<40cm$^{-1}$) are nor present in experimental sample. Possible reasons for this are discussed.}, note = {in calculations tRNA-Phe was used}} [ AT ]ARTICLE{Harvey93, author = "Harvey, S. C.; Gabb, H. A.", title = {Conformational transitions using molecular dynamics with minimum biasing}, journal = Biopolymers, year = 1993, volume = 33, pages = "1167-1172", abstract = {The molecular dynamics algorithm (MD), which simulates intramolecular motions on the subnanosecond timescale, has been modified to allow the investigation of slow conformational transitions that do not necessarily occur spontaneously in MD simulations. The method is designated CONTRA MD (CONformational TRAnsitions by Molecular Dynamics with minimum biasing). The method requires the prior definition of a single conformational variable that is required to vary monotonically from an initial conformation to a final target conformation. The simulation is broken up into a series of short free MD segments, and we determine, after each segment of MD, whether or not the system has evolved toward the final conformation. Those segments that do not move the system in that direction are deleted. Those that do move it toward the final conformation are patched together sequentially to generate a single representative trajectory along the transition pathway. The CONTRA MD method is demonstrated first by application to the simultaneous C2'-endo to C3'-endo repucker and anti to syn N-glycosidic torsion transitions in 2'-deoxyadenosine and then to the large-scale bending in phenylalanine transfer RNA.}}