Packing Structures and Transitions in Liquids and Solids

Stillinger, Frank H.; Weber, Thomas A.

doi:10.1126/science.225.4666.983

Cited by 977 publications

(708 citation statements)

References 15 publications

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“…In the present work, the trajectories were quenched to examine the structure of the underlying potential energy surface (Stillinger & Weber, 1984;Elber & Karplus, 1987;Troyer & Cohen, 1995). The results provide insight into the origin of the conformational distributions seen in the room temperature trajectories, in terms of the location of the minima which serve as the basins of attraction.…”

Section: Discussionmentioning

confidence: 97%

“…Thus far, we have considered the extent of the conformational space that is sampled by the molecular dynamics trajectories at a temperature of 300 K. Information about the features of the underlying potential energy surface (PES) is provided by quenching the trajectories to remove their kinetic energy (Stillinger & Weber, 1984;Levitt, 1985;Elber & Karplus, 1987;Ohmine, 1995;Troyer & Cohen, 1995). This technique probes the minima on the adiabatic PES.…”

Section: The Underlying Potential Energy Suflacementioning

confidence: 99%

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Locally accessible conformations of proteins: Multiple molecular dynamics simulations of crambin

1998

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Multiple molecular dynamics (MD) simulations of crambin with different initial atomic velocities are used to sample conformations in the vicinity of the native structure. Individual trajectories of length up to 5 ns sample only a fraction of the conformational distribution generated by ten independent 120 ps trajectories at 300 K. The backbone atom conformational space distribution is analyzed using principal components analysis (PCA). Four different major conformational regions are found. In general, a trajectory samples only one region and few transitions between the regions are observed. Consequently, the averages of structural and dynamic properties over the ten trajectories differ significantly from those obtained from individual trajectories. The nature of the conformational sampling has important consequences for the utilization of MD simulations for a wide range of problems, such as comparisons with X-ray or NMR data. The overall average structure is significantly closer to the X-ray structure than any of the individual trajectory average structures. The high frequency (less than 10 ps) atomic fluctuations from the ten trajectories tend to be similar, but the lower frequency (100 ps) motions are different. To improve conformational sampling in molecular dynamics simulations of proteins, as in nucleic acids, multiple trajectories with different initial conditions should be used rather than a single long trajectory.

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Section: Discussionmentioning

confidence: 97%

Section: The Underlying Potential Energy Suflacementioning

confidence: 99%

Locally accessible conformations of proteins: Multiple molecular dynamics simulations of crambin

1998

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“…This strategy of classifying potential energy minima resembles that used by Stillinger and Weber to study inherent structures in liquids. 76 Figure 4 shows the probability distribution of different order parameters along the reaction coordinate obtained from the quenched trajectory. Qualitatively, these probability distribution plots can be compared to a coarse-grained potential of mean force along the reaction coordinate as reported independently by transition path sampling.…”

Section: Orchestrated Order Of Events During Pol Closingmentioning

confidence: 99%

Conformational Transition Pathway of Polymerase β/DNA upon Binding Correct Incoming Substrate

Arora

Schlick

2005

J. Phys. Chem. B

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The closing conformational transition of wild-type polymerase bound to DNA template/primer before the chemical step (nucleotidyl transfer reaction) is simulated using the stochastic difference equation (in length version, "SDEL") algorithm that approximates long-time dynamics. The order of the events and the intermediate states during pol 's closing pathway are identified and compared to a separate study of pol using transition path sampling (TPS) (Radhakrishnan, R.; Schlick, T. Proc. Natl. Acad. Sci. USA 2004, 101, 5970-5975). Results highlight the cooperative and subtle conformational changes in the pol active site upon binding the correct substrate that may help explain DNA replication and repair fidelity. These changes involve key residues that differentiate the open from the closed conformation (Asp192, Arg258, Phe272), as well as residues contacting the DNA template/primer strand near the active site (Tyr271, Arg283, Thr292, Tyr296) and residues contacting the and γ phosphates of the incoming nucleotide (Ser180, Arg183, Gly189). This study compliments experimental observations by providing detailed atomistic views of the intermediates along the polymerase closing pathway and by suggesting additional key residues that regulate events prior to or during the chemical reaction. We also show general agreement between two sampling methods (the stochastic difference equation and transition path sampling) and identify methodological challenges involved in the former method relevant to large-scale biomolecular applications. Specifically, SDEL is very quick relative to TPS for obtaining an approximate path of medium resolution and providing qualitative information on the sequence of events; however, associated free energies are likely very costly to obtain because this will require both successful further refinement of the path segments close to the bottlenecks and large computational time.

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“…Biomolecular clusters are exciting study objects for future matter wave experiments as they permit one to scale the mass in well-defined steps, while at the same time changing the internal properties in an intriguing way: the number of possible conformations as well as the number of allowed configurational and vibrational transitions scales exponentially with the size of the cluster [13], and it is still an open question how this will affect de Broglie interferometry [14], which formally considers only the center of mass motion alone. (19].…”

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confidence: 99%

Gas-phase formation of large neutral alkaline-earth metal tryptophan complexes

Marksteiner

Haslinger

Sclafani

et al. 2008

J. Am. Soc. Mass Spectrom.

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We report on the first observation of isolated large neutral metal amino acid complexes such as TrpnMek, with Me == Ca, Ba, Sr, cluster combinations covering n = 1. ..33, k = 0..2 and masses beyond 6500 u. The cluster beam is generated using UV laser desorption from a mixed powder of alkaline-earth metal salts and tryptophan inside a cluster mixing chalU1el. The particles are detected using VUV photoionization followed by time-of-flight mass spectroscopy. The enhanced stability of metal amino acid clusters over pure amino acid clusters is substantiated in molecular dynamics simulations by determining the gain in binding energy related to the inclusion of the metal atoms. . The majority of studies so far focused on the generation and use of ionic species. Our work, presented here, focuses on the gas-phase formation of neutral biomolecular clusters as did already some very early studies in the field [1]. Such experiments are often motivated by the desire to better identify the role of solvation and desolvation for the relative importance of various binding forces in organic clusters and molecules [5].The particle's neutrality is also an important criterion in efforts to establish new beam methods for quantum interferometry with molecular matter waves [6-9] as well as for precision metrology on large molecules [10][11][12]. Neutral molecules are much better isolated from any electromagnetic environment and they may therefore propagate coherently, without noticeable perturbation, even in a rather noisy field environment.Biomolecular clusters are exciting study objects for future matter wave experiments as they permit one to scale the mass in well-defined steps, while at the same time changing the internal properties in an intriguing way: the number of possible conformations as well as the number of allowed configurational and vibrational transitions scales exponentially with the size of the cluster [13], and it is still an open question how this will affect de Broglie interferometry [14], which formally considers only the center of mass motion alone. (19]. But it has still remained a challenge to find reproducible methods for photoionizing biomolecules and complexes with masses exceeding 3000 u [17,20,21].The formation and photo-detection of small amino acid [22] and nucleotide clusters [23], both hydrated and solvent-free, were already reported for objects up to 1400 u. Ultracold small bioclusters can be formed by pick-up in helium nano-droplets [24]. Complexes formed between metal atoms and amino acids were also studied to understand their structure [25], their fragmentation pathways [26,27], and metal ion affinities [28].Here we extend these investigations to much larger organometallic complexes composed of up to more than 30 tryptophan molecules with masses exceeding 6500 u, that can still be detected using VUV photoionization and time-of-flight mass spectrometry. ExperimentalWe generate the molecular macroclusters using pulsed laser evaporation and collisional cooling: the pulsed beam of aNd:YAG laser (Quantel...

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Packing Structures and Transitions in Liquids and Solids

Cited by 977 publications

References 15 publications

Locally accessible conformations of proteins: Multiple molecular dynamics simulations of crambin

Locally accessible conformations of proteins: Multiple molecular dynamics simulations of crambin

Conformational Transition Pathway of Polymerase β/DNA upon Binding Correct Incoming Substrate

Gas-phase formation of large neutral alkaline-earth metal tryptophan complexes

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