Advances in biomolecular simulations: methodology and recent applications

Norberg, Jan; Nilsson, Lennart

doi:10.1017/s0033583503003895

Cited by 131 publications

(99 citation statements)

References 329 publications

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“…The development of implicit solvent approaches is widespread, and has allowed investigators to address larger systems or longer timescale phenomena such as ligand binding and conformational change with increasing confidence (45,23). However, the most detailed view currently attainable of certain molecular processes at the atomic level is undeniably provided by explicit solvent simulations, despite the limitations that such approaches themselves remain approximations (typically using non-polarizable atoms, for example) and that long time scale events can only be observed infrequently or not at all.…”

Section: Obp-thymol Dynamics In Explicit Solventmentioning

confidence: 99%

Odorant Binding and Conformational Dynamics in the Odorant-binding Protein

Hajjar

Pérahia

Débat

et al. 2006

Journal of Biological Chemistry

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In mammals, the olfactory epithelium secretes odorantbinding proteins (OBPs), which are lipocalins found freely dissolved in the mucus layer protecting the olfactory neurons. OBPs may act as passive transporters of predominantly hydrophobic odorant molecules across the aqueous mucus layer, or they may play a more active role in which the olfactory neuronal receptor recognizes the OBP-ligand complex. To better understand the molecular events accompanying the initial steps in the olfaction process, we have performed molecular dynamics studies of rat and pig OBPs with the odorant molecule thymol. These calculations provide an atomic level description of conformational changes and pathway intermediates that remain difficult to study directly. A series of eight independent molecular dynamics trajectories of rat OBP permitted the observation of a consensus pathway for ligand unbinding and the calculation of the potential of mean force (PMF) along this path. Titration microcalorimetry confirmed the specific binding of thymol to this protein with a strong hydrophobic component. In both rat and pig OBPs we observed lipocalin strand pair opening in the presence of ligand, consistent with potential roles of these proteins in olfactive receptor recognition.

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Section: Obp-thymol Dynamics In Explicit Solventmentioning

confidence: 99%

Odorant Binding and Conformational Dynamics in the Odorant-binding Protein

Hajjar

Pérahia

Débat

et al. 2006

Journal of Biological Chemistry

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“…number of interaction sites per coarse-grained body. There have been several different procedures for efficiently calculating the non-bonded interactions and recent reports of gain in efficiency [47] are encouraging. Notable improvements include faster non-bonded electrostatics calculations via meshing [1][2], and use of tabulation and bitmapping schemes [48].…”

Section: Interaction Forcesmentioning

confidence: 99%

Substructured molecular dynamics using multibody dynamics algorithms

Mukherjee

Plimpton

Anderson

2008

International Journal of Non-Linear Mechanics

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This paper presents results obtained from simulating several biomolecular and bulk materials using multibody dynamics algorithms. The systems studied include bulk water, alkane chains, alanine dipeptide and carboxyl terminal fragments of calmodulin, ribosomal protein, and rhodopsin. The atomistic representations of these systems include several thousand degrees of freedom and the results of nano-second long simulations of several of these systems are presented. The stability and validity of the simulations are studied through conservation of energy, thermodynamics properties and conformational analysis. In these simulations, a speed up of an order of magnitude is realized for conservative error bounds with a fixed time step integration scheme. A discussion is presented on the open-source software developed to facilitate future research using multibody dynamics with molecular dynamics.

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“…We have to develop (algorithmic) models reflecting molecular pathways and have to look deeper into cellular networks to understand data from comprehensive large-scale genomics or proteomics experiments [12,13]. Progress in understanding cell biological mechanisms will facilitate drug development for the treatment of complex diseases, and will eventually lead to personalised medicine.…”

Section: Trends In Technology Development For the Biology Of The Futurementioning

confidence: 99%

Genome Projects and the Functional-Genomic Era

Sauer

Konthur

Lehrach

2005

CCHTS

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The problems we face today in public health as a result of the -fortunately -increasing age of people and the requirements of developing countries create an urgent need for new and innovative approaches in medicine and in agronomics. Genomic and functional genomic approaches have a great potential to at least partially solve these problems in the future. Important progress has been made by procedures to decode genomic information of humans, but also of other key organisms. The basic comprehension of genomic information (and its transfer) should now give us the possibility to pursue the next important step in life science eventually leading to a basic understanding of biological information flow; the elucidation of the function of all genes and correlative products encoded in the genome, as well as the discovery of their interactions in a molecular context and the response to environmental factors. As a result of the sequencing projects, we are now able to ask important questions about sequence variation and can start to comprehensively study the function of expressed genes on different levels such as RNA, protein or the cell in a systematic context including underlying networks. In this article we review and comment on current trends in large-scale systematic biological research. A particular emphasis is put on technology developments that can provide means to accomplish the tasks of future lines of functional genomics.

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Advances in biomolecular simulations: methodology and recent applications

Cited by 131 publications

References 329 publications

Odorant Binding and Conformational Dynamics in the Odorant-binding Protein

Odorant Binding and Conformational Dynamics in the Odorant-binding Protein

Substructured molecular dynamics using multibody dynamics algorithms

Genome Projects and the Functional-Genomic Era

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