The Sanbonmatsu Team

Welcome to the Sanbonmatsu Team

Recent Publications.

60.Regulation of the Mammalian Elongation Cycle by Subunit Rolling: A Eukaryotic-Specific Ribosome Rearrangement

Tatyana V Budkevich, Jan Giesebrecht, Elmar Behrmann, Justus Loerke, David JF Ramrath, Thorsten Mielke, Jochen Ismer, Peter W Hildebrand, Chang-Shung Tung, Knud H Nierhaus, Karissa Y Sanbonmatsu, Christian MT Spahn

Cell 158 (1), 121-131, 2014

The extent to which bacterial ribosomes and the significantly larger eukaryotic ribosomes share the same mechanisms of ribosomal elongation is unknown. Here, we present subnanometer resolution cryoelectron microscopy maps of the mammalian 80S ribosome in the posttranslocational state and in complex with the eukaryotic eEF1A⋅ Val-tRNA⋅ GMPPNP ternary complex, revealing significant differences in the elongation mechanism between bacteria and mammals. Surprisingly, and in contrast to bacterial ... ------------------------------------------------------------------------------------

59. Flipping through the Genetic Code: New Developments in Discrimination between Cognate and Near-Cognate tRNAs and the Effect of Antibiotics

KY Sanbonmatsu Journal of molecular biology 426 (19), 3197-3200, 2014

The ribosome is responsible for implementing the genetic code by reading instructions encoded in mRNA and manufacturing the corresponding protein [1], [2] and [3]. The suite of tRNAs act as a molecular look-up table, converting the 4-letter alphabet of nucleic acids to the 20-letter alphabet of proteins. Reading the mRNA similar to a ticker tape, for each 3-nucleotide codon, the ribosome must select the tRNA carrying the corresponding amino acid and reject all other tRNAs. This is a difficult task, as the ribosome is immersed in a sea of incorrect ...

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58. Dynamics of riboswitches: Molecular simulations

Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms, 2014

Riboswitch RNAs play key roles in bacterial metabolism and represent a promising new class of antibiotic targets for treatment of infectious disease. While many studies of riboswitches have been performed, the exact mechanism of riboswitch operation is still not fully understood at the atomistic level of detail. Molecular dynamics simulations are useful for interpreting existing experimental data and producing predictions for new experiments. Here, a wide range of computational studies on riboswitches is reviewed. By elucidating ...

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57. Cryo-EM structure of the small subunit of the mammalian mitochondrial ribosome

Prem S Kaushal, Manjuli R Sharma, Timothy M Booth, Emdadul M Haque, Chang-Shung Tung, Karissa Y Sanbonmatsu, Linda L Spremulli, Rajendra K Agrawal

Proceedings of the National Academy of Sciences 111 (20), 7284-7289, 2014

The mammalian mitochondrial ribosomes (mitoribosomes) are responsible for synthesizing 13 membrane proteins that form essential components of the complexes involved in oxidative phosphorylation or ATP generation for the eukaryotic cell. The mammalian 55S mitoribosome contains significantly smaller rRNAs and a large mass of mitochondrial ribosomal proteins (MRPs), including large mito-specific amino acid extensions and insertions in MRPs that are homologous to bacterial ribosomal proteins ...

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56. Reduced Model Captures Magnesium-RNA Interaction Free Energy of Riboswitches

SRyan L Hayes, Jeffrey K Noel, Paul C Whitford, Udayan Mohanty, Karissa Y Sanbonmatsu, José N Onuchic

Biophysical journal 106 (7), 1508-1519, 2014 /p>

The stability of RNA tertiary structures depends heavily on Mg2+. The Mg2+-RNA interaction free energy that stabilizes an RNA structure can be computed experimentally through fluorescence-based assays that measure Γ2+, the number of excess Mg2+ associated with an RNA molecule. Previous explicit-solvent simulations predict that the majority of excess Mg2+ ions interact closely and strongly with the RNA, unlike monovalent ions such as K+, suggesting that an explicit treatment of Mg2+ is important for capturing ...

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55.Rise of the RNA machines: structural probing of long non-coding RNAs.

IV Novikova, SP Hennelly and KY Sanbonmatsu.Journal of Molecular Biology

Journal of Molecular Biology, 425(19)3731-3746, 2013

(5 citation)

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54.3S: Shotgun Secondary Structure determination for long non-coding RNAs,

IV Novikova, A Dharap, SP Hennelly, KY Sanbonmatsu

Methods, 63 (2), 170-177, 2013.

Long non-coding RNAs (lncRNAs) have emerged as an important class of RNAs playing key roles in development, disease and epigenetics. Knowledge of lncRNA structure may be critical in understanding function for many lncRNA systems. Due to the enormous number of possible folds for these sequences, secondary structure determination presents a significant challenge, both experimentally and computationally.

(2 citation)

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53.Tackling structures of long noncoding RNAs

IV Novikova, SP Hennelly, KY Sanbonmatsu.

International Journal of Molecular Science 14 (12), 23672-23684, 2013.

RNAs are important catalytic machines and regulators at every level of gene expression. A new class of RNAs has emerged called long non-coding RNAs, providing new insights into evolution, development and disease. Long non-coding RNAs (lncRNAs) predominantly found in higher eukaryotes, have been implicated in the regulation of transcription factors, chromatin-remodeling, hormone receptors and many other processes.

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52.Simulating movement of tRNA through the ribosome during hybrid-state formation

PC Whitford, KY Sanbonmatsu,

Journal of chemical physics 139, 121919, 2013.

Biomolecular simulations provide a means for exploring the relationship between flexibility, energetics, structure, and function. With the availability of atomic models from X-ray crystallography and cryoelectron microscopy (cryo-EM), and rapid increases in computing capacity, it is now possible to apply molecular dynamics (MD) simulations to large biomolecular machines, and systematically partition the factors that contribute to function.

(1 citation)

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51.Connecting the Kinetics and Energy Landscape of tRNA Translocation on the Ribosome

PC Whitford, SC Blanchard, JHD Cate, KY Sanbonmatsu,

PLoS computational biology 9 (3), e1003003, 2013.

Functional rearrangements in biomolecular assemblies result from diffusion across an underlying energy landscape. While bulk kinetic measurements rely on discrete state-like approximations to the energy landscape, single-molecule methods can project the free energy onto specific coordinates.

(4 citation)

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50.The expression platform and the aptamer: cooperativity between Mg2+ and ligand in the SAM-I riboswitch.

SP Hennelly, IV Novikova, KY Sanbonmatsu, .

Nucleic acids research 41 (3), 1922-1935, 2013.

Riboswitch operation involves the complex interplay between the aptamer domain and the expression platform. During transcription, these two domains compete against each other for shared sequence. In this study, we explore the cooperative effects of ligand binding and Magnesium interactions in the SAM-I riboswitch in the context of aptamer collapse and anti-terminator formation.

(3 citation)

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49. Structural architecture of the human long non-coding RNA, steroid receptor RNA activator.

IV Novikova, SP Hennelly, KY Sanbonmatsu.

Nucleic Acids Research, 40 (11), 5034-5051, 2012

While functional roles of several long non-coding RNAs (lncRNAs) have been determined, the molecular mechanisms are not well understood. Here, we report the first experimentally derived secondary structure of a human lncRNA, the steroid receptor RNA activator (SRA), 0.87 kB in size.

(32 citation)

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48. Molecular Dynamics Simulations of the Ribosome

KY Sanbonmatsu, SC Blanchard, PC Whitford

Biophysical approaches to translational control of gene expression, 51-68,2013

Structural biology techniques such as crystallography and cryo-EM produce high resolution snap shots of the ribosome at various stages of protein synthesis. Single molecule studies yield time-resolved measurements with low spatial resolution.

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47. Sizing up long non-coding RNAs: Do lncRNAs have secondary and tertiary structure

Irina V. Novikova, Scott P. Hennelly and Karissa Y. Sanbonmatsu.

Bio Architecture,2012

Long noncoding RNAs (lncRNAs) play a key role in many important areas of epigenetics, stem cell biology, cancer, signaling and brain function. This emerging class of RNAs constitutes a large fraction of the transcriptome, with thousands of new lncRNAs reported each year.

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46. Magnesium Fluctuations Modulate RNA Dynamics in the SAM-I Riboswitch

RL Hayes, JK Noel, U Mohanty, PC Whitford, SP Hennelly, JN Onuchic, KY Sanbonmatsu

Journal of the American Chemical Society 134 (29), 12043-12053, 2012

Experiments demonstrate that Mg2+ is crucial for structure and function of RNA systems, yet the detailed molecular mechanism of Mg2+ action on RNA is not well understood. We investigate the interplay between RNA and Mg2+ at atomic resolution through ten 2-μs explicit solvent molecular dynamics simulations of the SAM-I riboswitch with varying ion concentrations.

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45. Biomolecular dynamics: order–disorder transitions and energy landscapes

PC Whitford, KY Sanbonmatsu, JN Onuchic

Reports on Progress in Physics 75 (7), 076601, 2012

While the energy landscape theory of protein folding is now a widely accepted view for understanding how relatively weak molecular interactions lead to rapid and cooperative protein folding, such a framework must be extended to describe the large-scale functional motions observed in molecular machines.

(1 citation)

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44. Structural architecture of the human long non-coding RNA, steroid receptor RNA activator

IV Novikova, SP Hennelly, KY Sanbonmatsu

Nucleic Acids Research 40 (11), 5034-5051,2012

(2 citation)

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43. Computational studies of molecular machines: the ribosome

KY Sanbonmatsu

Current opinion in structural biology, 2012

The past decade has produced an avalanche of experimental data on the structure and dynamics of the ribosome. Groundbreaking studies in structural biology and kinetics have placed important constraints on ribosome structural dynamics. However, a gulf remains between static structures and time dependent data. In particular, X-ray crystallography and cryo-EM studies produce static models of the ribosome in various states, but lack dynamic information.

(2 citation)

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42. Excited states of ribosome translocation revealed through integrative molecular modeling

PC Whitford, A Ahmed, Y Yu, SP Hennelly, F Tama, CMT Spahn, JN Onuchic, KY Sanbonmatsu

Proceedings of the National Academy of Sciences 108 (47), 18943-18948 ,2011

The dynamic nature of biomolecules leads to significant challenges when characterizing the structural properties associated with function. While X-ray crystallography and imaging techniques (such as cryo-electron microscopy) can reveal the structural details of stable molecular complexes, strategies must be developed to characterize configurations that exhibit only marginal stability (such as intermediates) or configurations that do not correspond to minima on the energy landscape (such as transition-state ensembles).

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41. Consensus among flexible fitting approaches improves the interpretation of cryo-EM data

A Ahmed, PC Whitford, KY Sanbonmatsu, F Tama

Journal of structural biology, 2011

Cryo-elecron microscopy (cryo-EM) can provide important structural information of large macromolecular assemblies in different conformational states. Recent years have seen an increase in structures deposited in the Protein Data Bank (PDB) by fitting a high-resolution structure into its low-resolution cryo-EM map.

(2 citation)

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40. Key intermolecular interactions in the E. coli 70S ribosome revealed by coarse-grained analysis

Z Zhang, KY Sanbonmatsu, GA Voth

Journal of the American Chemical Society 133 (42), 16828-16838, 2011

The ribosome is a very large complex that consists of many RNA and protein molecules and plays a central role in protein biosynthesis in all organisms. Extensive interactions between different molecules are critical to ribosomal functional dynamics. In this work, intermolecular interactions in the Escherichia coli 70S ribosome are investigated by coarse-grained (CG) analysis.

(2 citation)

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39. Information Processing by Nanomachines

KY Sanbonmatsu, SC Blanchard, PC Whitford

Molecular Machines, 67, 2011

The ribosome is the most highly conserved molecular machine in the cell and has the responsibility of implementing the genetic code by converting the information residing in nucleic acid into protein.

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38. Tertiary contacts control switching of the SAM-I riboswitch

SP Hennelly, KY Sanbonmatsu

Nucleic Acids Research 39 , 2416-2431,2011

Riboswitches are non-coding RNAs that control gene expression by sensing small molecules through changes in secondary structure. While secondary structure and ligand interactions are thought to control switching, the exact mechanism of control is unknown. Using a novel two-piece assay that competes the anti-terminator against the aptamer, we directly monitor the process of switching.

(8 citation)

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37.Dynamic views of ribosome function: Energy landscapes and ensembles

PC Whitford, RB Altman, P Geggier, DS Terry, JB Munro, JN Onuchic, CMT Spahn, KY Sanbonmatsu, SC Blanchard

Ribosomes, 303-319, 2011

Single-molecule fluorescence resonance energy transfer (smFRET)(reviewed in Munro et al., 2009) and cryo-electron microscopy (cryo-EM) investigations (Frank and Spahn, 2006; Spahn and Penczek, 2009; Fischer et al., 2010) of the translation apparatus reveal the ribosome's propensity to undergo large-scale fluctuations in conformation during function.

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36.Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites

AH Ratje, J Loerke, A Mikolajka, M Brünner, PW Hildebrand, AL Starosta, A Dönhöfer, SR Connell, P Fucini, T Mielke, PC Whitford, JN Onuchic, Y Yu, KY Sanbonmatsu, RK Hartmann, PA Penczek, DN Wilson, CMT Spahn

Nature 468 (7324), 713-716, 2010

The elongation cycle of protein synthesis involves the delivery of aminoacyl-transfer RNAs to the aminoacyl-tRNA-binding site (A site) of the ribosome, followed by peptide-bond formation and translocation of the tRNAs through the ribosome to reopen the A site 1, 2. The translocation reaction is catalysed by elongation factor G (EF-G) in a GTP-dependent manner 3.

(44 citation)

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35. Connecting energy landscapes with experimental rates for aminoacyl-tRNA accommodation in the ribosome

PC Whitford, JN Onuchic, KY Sanbonmatsu

Journal of the American Chemical Society 132 (38), 13170, 2010

Using explicit-solvent simulations of the 70S ribosome, the barrier-crossing attempt frequency was calculated for aminoacyl-tRNA elbow-accommodation. In seven individual trajectories (200–300 ns, each), the relaxation time of tRNA structural fluctuations was determined to be~ 10 ns and the barrier-crossing attempt-frequency of tRNA accommodation is~ 1–10 µs− 1.

(9 citation)

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34.Free state conformational sampling of the SAM-I riboswitch aptamer domain

CD Stoddard, RK Montange, SP Hennelly, RP Rambo, KY Sanbonmatsu, RT Batey

Structure (London, England: 1993) 18 (7), 787, 2010

Summary Riboswitches are highly structured elements residing in the 5'untranslated region of messenger RNAs that specifically bind cellular metabolites to alter gene expression. While there are many structures of ligand bound riboswitches that reveal details of bimolecular recognition, their unliganded structures remain poorly characterized.

(43 citation)

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33.SMOG@ ctbp: simplified deployment of structure-based models in GROMACS

JK Noel, PC Whitford, KY Sanbonmatsu, JN Onuchic

Nucleic acids research 38 (suppl 2), W657-W661 30, 2010

Molecular dynamics simulations with coarse-grained and/or simplified Hamiltonians are an effective means of capturing the functionally important long-time and large-length scale motions of proteins and RNAs. Structure-based Hamiltonians, simplified models developed from the energy landscape theory of protein folding, have become a standard tool for investigating biomolecular dynamics.

(30 citation)

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32. Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways

PC Whitford, P Geggier, RB Altman, SC Blanchard, JN Onuchic, KY Sanbonmatsu

RNA 16 (6), 1196-1204, 2010

The ribosome is a massive ribonucleoprotein complex (∼ 2.4 MDa) that utilizes large-scale structural fluctuations to produce unidirectional protein synthesis. Accommodation is a key conformational change during transfer RNA (tRNA) selection that allows movement of tRNA into the ribosome. Here, we address the structure–function relationship that governs accommodation using all-atom molecular simulations and single- molecule fluorescence resonance energy transfer (smFRET).

(42 citation)

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31.Spontaneous formation of the unlocked state of the ribosome is a multistep process

JB Munro, RB Altman, CS Tung, JHD Cate, KY Sanbonmatsu, SC Blanchard

Proceedings of the National Academy of Sciences 107 (2), 709-714, 2010

The mechanism of substrate translocation through the ribosome is central to the rapid and faithful translation of mRNA into proteins. The rate-limiting step in translocation is an unlocking process that includes the formation of an “unlocked” intermediate state, which requires the convergence of large-scale conformational events within the ribosome including tRNA hybrid states formation, closure of the ribosomal L1 stalk domain, and subunit ratcheting.

(44 citation)

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30. A fast dynamic mode of the EF-G-bound ribosome

JB Munro, RB Altman, CS Tung, KY Sanbonmatsu, SC Blanchard

The EMBO journal 29 (4), 770-781, 2009

A key intermediate in translocation is an 'unlocked state'of the pre-translocation ribosome in which the P-site tRNA adopts the P/E hybrid state, the L1 stalk domain closes and ribosomal subunits adopt a ratcheted configuration. Here, through two-and three-colour smFRET imaging from multiple structural perspectives, EF-G is shown to accelerate structural and kinetic pathways in the ribosome, leading to this transition.

(32 citation)

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29. Navigating the ribosome's metastable energy landscape

JB Munro, KY Sanbonmatsu, CMT Spahn, SC Blanchard

Trends in biochemical sciences 34 (8), 390-400, 2009

The molecular mechanisms by which tRNA molecules enter and transit the ribosome during mRNA translation remains elusive. However, recent genetic, biochemical and structural studies offer important new findings into the ordered sequence of events underpinning the translocation process that help place the molecular mechanism within reach. In particular, new structural and kinetic insights have been obtained regarding tRNA movements through 'hybrid state'configurations.

(42 citation)

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28.Stochastic gating and drug–ribosome interactions

AC Vaiana, KY Sanbonmatsu

Journal of molecular biology 386 (3), 648-661 ,2009

Gentamicin is a potent antibiotic that is used in combination therapy for inhalation anthrax disease. The drug is also often used in therapy for methicillin-resistant Staphylococcusaureus. Gentamicin works by flipping a conformational switch on the ribosome, disrupting the reading head (ie, 16S ribosomal decoding bases 1492–1493) used for decoding messenger RNA.

(31 citation)

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27.Nonlocal helix formation is key to understanding S-adenosylmethionine-1 riboswitch function

PC Whitford, A Schug, J Saunders, SP Hennelly, JN Onuchic, KY Sanbonmatsu

Biophysical journal 96 (2), L7-L9, 2009

Riboswitches are noncoding RNAs that regulate gene expression in response to changing concentrations of specific metabolites. Switching activity is affected by the interplay between the aptamer domain and expression platform of the riboswitch. The aptamer domain binds the metabolite, locking the riboswitch in a ligand-bound conformation.

(36 citation)

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26. An all‐atom structure‐based potential for proteins: Bridging minimal models with all‐atom empirical forcefields

PC Whitford, JK Noel, S Gosavi, A Schug, KY Sanbonmatsu, JN Onuchic

Proteins: Structure, Function, and Bioinformatics 75 (2), 430-44 20081,2009

Protein dynamics take place on many time and length scales. Coarse-grained structure-based equation image models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution.

(65 citation)

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25. A new view of protein synthesis: Mapping the free energy landscape of the ribosome using single‐molecule FRET

JB Munro, A Vaiana, KY Sanbonmatsu, SC Blanchard

Biopolymers 89 (7), 565-577, 2008

This article reviews the application of single-molecule fluorescence resonance energy transfer (smFRET) methods to the study of protein synthesis catalyzed by the ribosome. smFRET is a powerful new technique that can be used to investigate dynamic processes within enzymes spanning many orders of magnitude. The application of wide- field smFRET imaging methods to the study of dynamic processes in the ribosome offers a new perspective on the mechanism of protein synthesis. Using this technique, the ...

(29 citation)

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24. Domain motions of Argonaute, the catalytic engine of RNA interference

D Ming, ME Wall, KY Sanbonmatsu

BMC bioinformatics 8 (1), 470, 2007

Background The Argonaute protein is the core component of the RNA-induced silencing complex, playing the central role of cleaving the mRNA target. Visual inspection of static crystal structures already has enabled researchers to suggest conformational changes of Argonaute that might occur during RNA interference.

(7 citation)

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23. High performance computing in biology: multimillion atom simulations of nanoscale systems

KY Sanbonmatsu, CS Tung

Journal of structural biology 157 (3), 470-480, 2007

Computational methods have been used in biology for sequence analysis (bioinformatics), all-atom simulation (molecular dynamics and quantum calculations), and more recently for modeling biological networks (systems biology). Of these three techniques, all-atom simulation is currently the most computationally demanding, in terms of compute load, communication speed, and memory load.

(96 citation)

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22. Large-scale simulations of the ribosome: a new landmark in computational biology

KY Sanbonmatsu, CS Tung

Journal of Physics: Conference Series 46 (1), 334, 2006

Within computational biology, all-atom simulation is the most computationally demanding field, in terms of compute load, communication speed, and memory load. Here, we report molecular dynamics simulation results for the ribosome, using 2.64 x106 atoms, the largest all-atom biomolecular simulation published to date.

(8 citation)

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21. Alignment/misalignment hypothesis for tRNA selection by the ribosome

Authors: KY Sanbonmatsu

Biochimie 88 (8), 1075-1089, 2006

Transfer RNAs (tRNAs) are the adaptor molecules that allow the ribosome to decode genetic information during protein synthesis. During decoding, the ribosome must chose the tRNA whose anticodon corresponds to the codon inscribed in the messenger RNA to incorporate the correct amino acid into the growing polypeptide chain. Fidelity is improved dramatically by a GTP hydrolysis event.

(20 citation)

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20. Energy landscape of the ribosomal decoding center

KY Sanbonmatsu

Biochimie 88 (8), 1053-1059, 2006

The ribosome decodes the genetic information that resides in nucleic acids. A key component of the decoding mechanism is a conformational switch in the decoding center of the small ribosomal subunit discovered in high-resolution X-ray crystallography studies. It is known that small subunit nucleotides A1492 and A1493 flip out of helix 44 upon transfer RNA (tRNA) binding; however, the operation principles of this switch remain unknown.

(27 citation)

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19. Using computer simulations to study decoding by the ribosome

K Sanbonmatsu

Computational Studies of RNA and DNA, 327-342, 2006

The ribosome is the central information-processing unit of the cell. Decoding is the step during protein synthesis where information is transferred from protein to nucleic acid. The decoding problem is reviewed, including recent kinetic, x-ray and cryo-EM data. Molecular dynamics simulations are described which investigate the role of hydrogen bond networks,“baseflipping” events, and changes in the conformation of transfer RNA.

(1 citation)

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18. Simulating movement of tRNA into the ribosome during decoding

KY Sanbonmatsu, S Joseph, CS Tung

Proceedings of the National Academy of Sciences of the United States of ... 2005

Decoding is the key step during protein synthesis that enables information transfer from RNA to protein, a process critical for the survival of all organisms. We have used large- scale (2.64× 10 6 atoms) all-atom simulations of the entire ribosome to understand a critical step of decoding. Although the decoding problem has been studied for more than four decades, the rate-limiting step of cognate tRNA selection has only recently been identified.

(162 citation)

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17. Atomic Model of the Thermus thermophilus 70S Ribosome Developed in Silico

CS Tung, KY Sanbonmatsu

Biophysical journal 87 (4), 2714-2722, 2004

The ribosome is a large molecular complex that consists of at least three ribonucleic acid molecules and a large number of proteins. It translates genetic information from messenger ribonucleic acid and makes protein accordingly. To better understand ribosomal function and provide information for designing biochemical experiments require knowledge of the complete structure of the ribosome.

(23 citation)

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16. Peptide folding simulations

S Gnanakaran, H Nymeyer, J Portman, KY Sanbonmatsu, AE Garcıa

Current opinion in structural biology 13 (2), 168-174, 2003

Developments in the design of small peptides that mimic proteins in complexity, recent advances in nanosecond time-resolved spectroscopy methods to study peptides and the development of modern, highly parallel simulation algorithms have come together to give us a detailed picture of peptide folding dynamics.

(172 citation)

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15. Understanding discrimination by the ribosome: Stability testing and groove measurement of codon–anticodon pairs

KY Sanbonmatsu, S Joseph

Journal of molecular biology 328 (1), 33-472003, 2003

The ribosome must discriminate between correct and incorrect tRNAs with sufficient speed and accuracy to sustain an adequate rate of cell growth. Here, we report the results of explicit solvent molecular dynamics simulations, which address the mechanism of discrimination by the ribosome. The universally conserved 16S rRNA base A1493 and the kink in mRNA between A and P sites amplify differences in stability between cognate and near-cognate codon–anticodon pairs.

(48 citation)

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14. All-atom homology model of the Escherichia coli 30S ribosomal subunit

CS Tung, S Joseph, KY Sanbonmatsu

Nature Structural & Molecular Biology 9 (10), 750-755, 2002

Understanding the structural basis of ribosomal function requires close comparison between biochemical and structural data. Although a large amount of biochemical data are available for the Escherichia coli ribosome, the structure has not been solved to atomic resolution. Using a new RNA homology procedure, we have modeled the all-atom structure of the E. coli 30S ribosomal subunit.

(41 citation)

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13. α-Helical stabilization by side chain shielding of backbone hydrogen bonds

AE García, KY Sanbonmatsu

Proceedings of the National Academy of Sciences 99 (5), 2782-2787, 2002

We study atomic models of the thermodynamics of the structural transition of peptides that form α-helices. The effect of sequence variation on α-helix formation for alanine-rich peptides, Ac-Ala 21-methyl amide (A21) and Ac-A 5 (AAARA) 3 A-methyl amide (Fs peptide), is investigated by atomic simulation studies of the thermodynamics of the helix- coil transition in explicit water.

(321 citation)

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12. Structure of Met‐enkephalin in explicit aqueous solution using replica exchange molecular dynamics

KY Sanbonmatsu, AE Garcia

Proteins: Structure, Function, and Bioinformatics 46 (2), 225-234, 2002

Replica exchange molecular dynamics (MD) simulations of Met-enkephalin in explicit solvent reveal helical and nonhelical structures. Four predominant structures of Met- enkephalin are sampled with comparable probabilities (two helical and two nonhelical). The energy barriers between these configurations are low, suggesting that Met-enkephalin switches easily between configurations.

(197 citation)

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11. Quasi-linear Zakharov simulations of Langmuir turbulence at rocket altitudes in the auroral ionosphere

KY Sanbonmatsu, DL Newman, MV Goldman

Journal of geophysical research 106 (A6), 10,519-10,535 2, 2001

A quasi-linear Zakharov simulation model has been constructed to study intense Langmuir waves and precipitating field-aligned electrons observed in the auroral ionosphere at altitudes below 1000 km. This self-consistent model couples the magnetized Zakharov equations to a modified quasi-linear diffusion equation, which includes an advective term describing electrons streaming into the simulation region.

(2 citation)

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10. Shear Viscosity of Strongly Coupled Yukawa Systems on Finite Length Scales

KY Sanbonmatsu, MS Murillo

The Yukawa shear viscosity has been calculated using nonequilibrium molecular dynamics. Near the viscosity minimum, we find exponential decay consistent with the Navier-Stokes equation, with significant deviations on finite length scales for larger viscosity values. The viscosity is determined to be nonlocal on a scale length consistent with the correlation length, revealing the length scales necessary for obtaining transport coefficients in the hydrodynamic limit by nonequilibrium molecular dynamics methods.

Read More...

(40 citation)

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9. Exploring the energy landscape of a β hairpin in explicit solvent

AE García, KY Sanbonmatsu

Proteins: Structure, Function, and Bioinformatics 42 (3), 345-354, 2000

We studied the energy landscape of the peptide Ace-GEWTYDDATKTFTVTE-Nme, taken from the C-terminal fragment (41–56) of protein G, in explicit aqueous solution by a highly parallel replica-exchange approach that combines molecular dynamics trajectories with a temperature exchange Monte Carlo process.
3.0.CO;2-H/abstract?deniedAccessCustomisedMessage=&userIsAuthenticated=fa">Read More...

(290 citation)
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8. Laying a foundation for laser-plasma modeling for the national ignition facility

HX Vu, KY Sanbonmatsu, B Bezzerides, DF DuBois

Computer physics communications 127 (1), 71-90, 2000

Three multi-dimensional plasma simulation models for simulating parametric instabilities occurring in laser-produced plasmas are presented. These models are based on a common framework, henceforth referred to as reduced-description, in which the electromagnetic field is represented by three separate temporal envelopes in order to model parametric instabilities with high-frequency and low-frequency daughter waves.
Read More...

(2 citation)
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7. Simulations-Comparison of molecular dynamics and particle-in-cell simulations for strongly coupled plasmas

KY Sanbonmatsu, LE Thode, HX Vu, MS Murillo

Journal de Physique-Colloques 10 (5), 259-262, 2000

(4 citation)
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6. Quantitative comparison of reduced-description particle-in-cell and quasilinear-Zakharov models for parametrically excited Langmuir turbulence

KY Sanbonmatsu, HX Vu, DF DuBois, B Bezzerides

Physics of Plasmas 7, 2824, 2000

The effect of kinetic processes on the saturation of parametric instabilities in an electromagnetically driven plasma is investigated. A reduced-description particle-in-cell technique is used as a benchmark to test a new quasilinear-Zakharov model which accounts for electron heating due to Landau damping by coupling the quasilinear diffusion equation to the Zakharov equations.
Read More...

(12 citation)
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5. The effect of kinetic processes on Langmuir turbulence

KY Sanbonmatsu, HX Vu, B Bezzerides, DF DuBois

Physics of Plasmas 7, 1723, 2001

Kinetic processes are shown to be crucial in determining the saturation level of stimulated Raman scattering for regimes relevant to NOVA [Campbell et al., Fusion Technol.[bold 21], 1344 (1992)] and the National Ignition Facility [Lindl, Phys. Plasmas [bold 2], 3933 (1995)]. To investigate these kinetic effects, the Zakharov,
Read More...

(19 citation)
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4. New paradigm for the self-consistent modeling of wave-particle and wave-wave interactions in the saturation of electromagnetically driven parametric instabilities

KY Sanbonmatsu, HX Vu, DF DuBois, B Bezzerides

Physical review letters 82 (5), 932-935, 1999

We introduce two new and complementary simulation models, which have domains of quantitative agreement, for the self-consistent evolution of the electron distribution, Langmuir decay cascades, and Langmuir collapse. In our reduced-description particle-in-cell (RPIC) simulations, Langmuir decay cascades and cycles of collapse are seen for the first time in particle simulation.
Read More...

(33 citation)
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3.Non-Markovian electron diffusion in the auroral ionosphere at high Langmuir-wave intensities.

KY Sanbonmatsu, I Doxas, MV Goldman, DL Newman

Geophysical research letters 24 (7), 807-810, 1997

(5 citation)
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2. Nonlinear coupling of lower hybrid waves to the kinetic low-frequency plasma response in the auroral ionosphere

KY Sanbonmatsu, MV Goldman, DL Newman

Geophysical research letters 22 (17), 2397-2400, 1995

(2 citation)
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1. A distance determination for the supernova remnant G27. 4+ 0.0 and its central X-ray source

KY Sanbonmatsu, DJ Helfand

The Astronomical Journal 104, 2189-2192, 1992

(2 citation)