From:	Ryszard Czerminski <ryszard #*at*# worf.moldyn.com>
Date:	Mon, 24 Nov 1997 12:54:57 -0500 (EST)
Subject:	tRNA modelling: summary

---- 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.}}

 -AatT- 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 [...]}}

 -8 at 8- 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.}}

 -x- at -x- 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}}

 &$at$& 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@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.}}

 -8 at 8- ARTICLE{Westhof96a,
   author = "E. Westhof et al.",
   title = {},
   journal = Science,
   year = 1996,
   volume = 272,
   pages = "1343",
   abstract = {} }

 at.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.}}




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