NAFlex: a web server for the study of nucleic acid flexibility.

We present NAFlex, a new web tool to study the flexibility of nucleic acids, either isolated or bound to other molecules. The server allows the user to incorporate structures from protein data banks, completing gaps and removing structural inconsistencies. It is also possible to define canonical (average or sequence-adapted) nucleic acid structures using a variety of predefined internal libraries, as well to create specific nucleic acid conformations from the sequence. The server offers a variety of methods to explore nucleic acid flexibility, such as a colorless wormlike-chain model, a base-pair resolution mesoscopic model and atomistic molecular dynamics simulations with a wide variety of protocols and force fields. The trajectories obtained by simulations, or imported externally, can be visualized and analyzed using a large number of tools, including standard Cartesian analysis, essential dynamics, helical analysis, local and global stiffness, energy decomposition, principal components and in silico NMR spectra. The server is accessible free of charge from the mmb.irbbarcelona.org/NAFlex webpage

NAFlex: a web server for the study of nucleic acid flexibility.

9 pags, 3 figs. -- Supplementary data are available at the Publisher's webWe present NAFlex, a new web tool to study the flexibility of nucleic acids, either isolated or bound to other molecules. The server allows the user to incorporate structures from protein data banks, completing gaps and removing structural inconsistencies. It is also possible to define canonical (average or sequence-adapted) nucleic acid structures using a variety of predefined internal libraries, as well to create specific nucleic acid conformations from the sequence. The server offers a variety of methods to explore nucleic acid flexibility, such as a colorless wormlike-chain model, a base-pair resolution mesoscopic model and atomistic molecular dynamics simulations with a wide variety of protocols and force fields. The trajectories obtained by simulations, or imported externally, can be visualized and analyzed using a large number of tools, including standard Cartesian analysis, essential dynamics, helical analysis, local and global stiffness, energy decomposition, principal components and in silico NMR spectra. The server is accessible free of charge from the mmb.irbbarcelona.org/NAFlex webpage.Funding for open access charge: Spanish Ministerio de Economía y Competitividad [BIO2012-3286]; European Research Council Advanced Grant (ERC); Instituto Nacional de Bioinformática (INB); Consolider E-Science Project; EU-Scalalife project; Fundación Marcelino Botín; European Union’s Seventh Framework Programme (FP7/2007–2013) [275096 to R.C.-G. and M.O.]

Model predictions showing the dependence of G6P concentrations on HK and PFK limiting rates.

<p>The proportional dysregulation predicts the broken grey line. The shades in the panels report the predicted G6P concentrations when the limiting rates of HK and PFK do not change proportionally. Solid black lines correspond to the model predictions for different levels of pre-incubation with Cu²⁺ (A), Cd²⁺ (B) and Hg²⁺ (C): they indicate how the metals change the limiting rates of the two enzymes and the consequent changes in metabolite concentrations. The same plot is for F6P, as G6P and F6P are in rapid equilibrium through the reaction catalysed by GPI.</p

Schemes for mechanisms of enzyme irreversible inhibition.

<p>Mechanisms of irreversible inhibition of HK activity and PFK activity by Hg²⁺ (A) and Cd²⁺ (B). <i>E</i> represents HK or PFK, <i>S</i> the respective substrate, <i>ES_n</i> the enzyme-substrate complex (HK follows a Michaelis-Menten equation (n = 1), whilst PFK is an allosteric enzyme (n>1)). <i>P</i> represents the products of the respective reactions, <i>X</i> the metal ions (Cd²⁺ or Hg²⁺), whilst <i>n</i> is the number of substrate binding sites and <i>m</i>+1 is the number of metal ion (<i>X</i>) molecules that can be bound irreversibly to the enzyme. The best agreement to the experimental results was obtained with m = 1 for HK and m = 2 for PFK.</p

Position for most relevant candidates to irreversible inhibition.

<p>(A) Cys 581 and Cys 794 on intersubunit interface of HK, (B) Cys 233 near to ATP binding site on PFK.</p

Scheme of the kinetic model.

<p>The scheme, equations and parameter values correspond to the kinetic model published previously <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080018#pone.0080018-Puigjaner1" target="_blank">[25]</a>. Parameters for HK: <i>K_M</i> = 0.40 mM, <i>K_i</i> = 0.11 mM. Parameters for GPI: <i>V^f_GPI</i> = 12474 nmol mg prot⁻¹ min⁻¹, <i>V^b_GPI</i> = 18125 nmol mg prot⁻¹ min⁻¹, <i>K_MS</i> = 0.48 mM, <i>K_MP</i> = 0.27 mM. Parameters for PFK: <i>K_S</i> = 0.061 mM, <i>h</i> = 1.47. Parameters for ALD: <i>V_ALD</i> = 6000 nmol mg prot⁻¹ min⁻¹, <i>K_M</i> = 0.13 mM. Limiting rates for HK (<i>V_HK</i>) and PFK (<i>V_PFK</i>) decrease at increasing values for Hg²⁺ and Cd²⁺ following <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080018#pone.0080018.e001" target="_blank">equations (1)</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0080018#pone.0080018.e002" target="_blank">(2)</a>, respectively for Hg²⁺ and Cd²⁺, with <i>V⁰_HK</i> = 63.0 nmol mg prot⁻¹ min⁻¹ and <i>V⁰_PFK</i> = 434 nmol mg prot⁻¹ min⁻¹.</p