Deformation of thiolated nucleic acid deposited on a silicon surface: A Static Mode approach

Brut, Mihaela; Estève, Alain; Landa, Georges; Renvez, Guillaume; Rouhani, M. Djafari; Vaisset, Marc; Gauchard, David

doi:10.1016/j.mseb.2009.11.014

Cited by 4 publications

(4 citation statements)

References 16 publications

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“…In this paper, we demonstrate that our static mode approach, after being presented and exposed on various molecular targets, ,,− enables concentrating all the information required for studying biomechanical properties at large within a costless framework in terms of calculation time and an infinite capability of considering biomolecular excitation. Through this study, thanks to the static mode method, we have rapidly collected many essential properties of a model system, namely, HIV-1 PR, properties already derived from multiple experimental or computational methods during the last 20 years.…”

Section: Discussionmentioning

confidence: 99%

“…Anharmonic effects could be introduced using matrices of higher order. Details about the method have already been published and partial results on several biomolecules reported. − In particular, we have successfully quantitatively correlated results to experiments, and probed active site stability and mutation effects on enzymatic activity . The static mode method allows calculating all the deformations of a molecule submitted to elementary external excitations.…”

Section: Methodsmentioning

confidence: 99%

“…For this reason, HIV-1 PR constitutes a good model system making it possible for us to validate the predictive nature of our method as well as to illustrate its potential beyond state of the art. In particular, we show how our static modes − can be post-treated in an interactive manner to design complex excitations. Through manipulation tools, an operator can design and evaluate an infinite set of single to multiple excitations, constraints, or interactions with no further computational cost.…”

Section: Introductionmentioning

confidence: 99%

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Toward in Silico Biomolecular Manipulation through Static Modes: Atomic Scale Characterization of HIV-1 Protease Flexibility

et al. 2014

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Probing biomolecular flexibility with atomic-scale resolution is a challenging task in current computational biology for fundamental understanding and prediction of biomolecular interactions and associated functions. This paper makes use of the static mode method to study HIV-1 protease considered as a model system to investigate the full biomolecular flexibility at the atomic scale, the screening of active site biomechanical properties, the blind prediction of allosteric sites, and the design of multisite strategies to target deformations of interest. Relying on this single calculation run of static modes, we demonstrate that in silico predictive design of an infinite set of complex excitation fields is reachable, thanks to the storage of the static modes in a data bank that can be used to mimic single or multiatom contact and efficiently anticipate conformational changes arising from external stimuli. All along this article, we compare our results to data previously published and propose a guideline for efficient, predictive, and custom in silico experiments.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Toward in Silico Biomolecular Manipulation through Static Modes: Atomic Scale Characterization of HIV-1 Protease Flexibility

et al. 2014

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“…In this work, we use a recently introduced method, the Static Modes method, − which makes it possible to efficiently screen the deformation response of a molecule submitted to an external excitation in a systematic manner. This method allows us to revisit some of the main enzyme biomechanical characteristics with an unpreceding atomic-scale degree of precision.…”

Section: Introductionmentioning

confidence: 99%

Atomic Scale Determination of Enzyme Flexibility and Active Site Stability through Static Modes: Case of Dihydrofolate Reductase

et al. 2011

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A Static Mode approach is used to screen the biomechanical properties of DHFR. In this approach, a specific external stimulus may be designed at the atomic scale granularity to arrive at a proper molecular mechanism. In this frame, we address the issues related to the overall molecular flexibility versus loop motions and versus enzymatic activity. We show that backbone motions are particularly important to ensure DHFR domain communication and notably highlight the role of a α-helix in Met20 loop motion. We also investigate the active site flexibility in different bound states. Whereas in the occluded conformation the Met20 loop is highly flexible, in the closed conformation backbone motions are no longer significant, the Met20 loop is rigidified by new intra- and intermolecular weak bonds, which stabilizes the complex and promotes the hydride transfer. Finally, while various simulations, including I14 V and I14A mutations, confirm that Ile14 is a key residue in catalytic activity, we isolate and characterize at the atomic scale how a specific intraresidue chemical group makes it possible to assist ligand positioning, to direct the nicotinamide ring toward the folate ring.

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Bringing aptamers into technologies: Impact of spacer terminations

Brut

Trapaidze

Estève

et al. 2012

Applied Physics Letters

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We propose a low cost modeling approach to screen the impact of aptamer structural modifications on their biomechanical stability. This responds to the current immature control of aptamer properties when integrated into bio-hybrid devices. We predict that common spacers (PEG, polythymine) disrupt aptamer rigidity, whereas alkyl chains have minimal incidence on its mechanical properties. We also observe that mutations in the active site are equally perturbative as PEG or polythymine. We suggest that the rational design of aptamer-based biosensing devices calls for a precise modeling of surface grafting and envision that our tool is readily adapted to face this challenge.

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Deformation of thiolated nucleic acid deposited on a silicon surface: A Static Mode approach

Cited by 4 publications

References 16 publications

Toward in Silico Biomolecular Manipulation through Static Modes: Atomic Scale Characterization of HIV-1 Protease Flexibility

Toward in Silico Biomolecular Manipulation through Static Modes: Atomic Scale Characterization of HIV-1 Protease Flexibility

Atomic Scale Determination of Enzyme Flexibility and Active Site Stability through Static Modes: Case of Dihydrofolate Reductase

Bringing aptamers into technologies: Impact of spacer terminations

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