Minimum sequence requirements for selective RNA‐ligand binding: A molecular mechanics algorithm using molecular dynamics and free‐energy techniques

In vitro evolution techniques allow RNA molecules with unique functions to be developed. However, these techniques do not necessarily identify the simplest RNA structures for performing their functions. Determining the simplest RNA that binds to a particular ligand is currently limited to experimental protocols. Here, we introduce a molecular‐mechanics based algorithm employing molecular dynamics simulations and free‐energy methods to predict the minimum sequence requirements for selective ligand binding to RNA. The algorithm involves iteratively deleting nucleotides from an experimentally determined structure of an RNA‐ligand complex, performing energy minimizations and molecular dynamics on each truncated structure, and assessing which truncations do not prohibit RNA binding to the ligand. The algorithm allows prediction of the effects of sequence modifications on RNA structural stability and ligand‐binding energy. We have implemented the algorithm in the AMBER suite of programs, but it could be implemented in any molecular mechanics force field parameterized for nucleic acids. Test cases are presented to show the utility and accuracy of the methodology. © 2006 Wiley Periodicals, Inc. J Comput Chem, 2006

[1]  Grant R. Zimmermann,et al.  Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA , 1997, Nature Structural Biology.

[2]  P. C. Anderson,et al.  Unusually short RNA sequences: design of a 13-mer RNA that selectively binds and recognizes theophylline. , 2005, Journal of the American Chemical Society.

[3]  Martina Rimmele,et al.  Nucleic Acid Aptamers as Tools and Drugs: Recent Developments , 2003, Chembiochem : a European journal of chemical biology.

[4]  L. Gold,et al.  Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. , 1990, Science.

[5]  P. Kollman,et al.  A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .

[6]  J. Åqvist,et al.  Ion-water interaction potentials derived from free energy perturbation simulations , 1990 .

[7]  S. Jayasena.  Aptamers: an emerging class of molecules that rival antibodies in diagnostics. , 1999, Clinical chemistry.

[8]  Roger A. Jones,et al.  Structural basis of RNA folding and recognition in an AMP–RNA aptamer complex , 1996, Nature.

[9]  T. Darden,et al.  Accurate crystal molecular dynamics simulations using particle-mesh-Ewald: RNA dinucleotides — ApU and GpC , 1995 .

[10]  D. Patel,et al.  RNA folding topology and intermolecular contacts in the AMP-RNA aptamer complex. , 1996, Biochemistry.

[11]  R. Zwanzig.  High‐Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases , 1954 .

[12]  E Westhof,et al.  Crystal structure of paromomycin docked into the eubacterial ribosomal decoding A site. , 2001, Structure.

[13]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[14]  Catherine Lozupone,et al.  Selection of the simplest RNA that binds isoleucine. , 2003, RNA.

[15]  D. Case,et al.  Theory and applications of the generalized born solvation model in macromolecular simulations , 2000, Biopolymers.

[16]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[17]  David R. Liu,et al.  Nucleic acid evolution and minimization by nonhomologous random recombination , 2002, Nature Biotechnology.

[18]  B. Sullenger,et al.  Developing aptamers into therapeutics. , 2000, The Journal of clinical investigation.

[19]  Peter A. Kollman,et al.  FREE ENERGY CALCULATIONS : APPLICATIONS TO CHEMICAL AND BIOCHEMICAL PHENOMENA , 1993 .

[20]  Lennart Nilsson,et al.  Molecular dynamics applied to nucleic acids. , 2002, Accounts of chemical research.

[21]  O. Uhlenbeck,et al.  In vitro selection of RNAs that undergo autolytic cleavage with Pb2+. , 1992, Biochemistry.

[22]  J. Szostak,et al.  Functional requirements for specific ligand recognition by a biotin-binding RNA pseudoknot. , 1998, Biochemistry.

[23]  P A Kollman,et al.  Molecular dynamics simulation of nucleic acids. , 2000, Annual review of physical chemistry.

[24]  Thomas E Cheatham,et al.  Simulation and modeling of nucleic acid structure, dynamics and interactions. , 2004, Current opinion in structural biology.

[25]  D. Patel,et al.  Structure, recognition and discrimination in RNA aptamer complexes with cofactors, amino acids, drugs and aminoglycoside antibiotics. , 2000, Journal of biotechnology.

[26]  D. Thirumalai,et al.  Kinetics of Folding of Proteins and RNA , 1996 .

[27]  Gerald F. Joyce,et al.  Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA , 1990, Nature.

[28]  J. Szostak,et al.  In vitro selection of RNA molecules that bind specific ligands , 1990, Nature.

[29]  O. Uhlenbeck,et al.  Keeping RNA happy. , 1995, RNA.

[30]  G. Ciccotti,et al.  Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .

[31]  Junmei Wang,et al.  Development and testing of a general amber force field , 2004, J. Comput. Chem..

[32]  D. Patel,et al.  Adaptive recognition by nucleic acid aptamers. , 2000, Science.

[33]  P. Kollman,et al.  Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate−DNA Helices , 1998 .

[34]  E. Westhof,et al.  Geometric nomenclature and classification of RNA base pairs. , 2001, RNA.

[35]  P. Higgs,et al.  Barrier heights between ground states in a model of RNA secondary structure , 1998 .

[36]  Michael R. Green,et al.  HIV-1 rev regulation involves recognition of non-Watson-Crick base pairs in viral RNA , 1991, Cell.

[37]  D. Turner,et al.  RNA structure prediction. , 1988, Annual review of biophysics and biophysical chemistry.

[38]  M. Famulok,et al.  Oligonucleotide aptamers that recognize small molecules. , 1999, Current opinion in structural biology.

[39]  P. Kollman,et al.  How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? , 2000 .

[40]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[41]  P. Higgs.  Thermodynamic properties of transfer RNA: a computational study , 1995 .

[42]  Irwin D Kuntz,et al.  Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods. , 2003, Biopolymers.