Development of polyphosphate parameters for use with the AMBER force field

Accurate force fields are essential for reproducing the conformational and dynamic behavior of condensed-phase systems. The popular AMBER force field has parameters for monophosphates, but they do not extend well to polyphorylated molecules such as ADP and ATP. This work presents parameters for the partial charges, atom types, bond angles, and torsions in simple polyphosphorylated compounds. The parameters are based on molecular orbital calculations of methyldiphosphate and methyltriphosphate at the RHF/6-31+G* level. The new parameters were fit to the entire potential energy surface (not just minima) with an RMSD of 0.62 kcal/mol. This is exceptional agreement and a significant improvement over the current parameters that produce a potential surface with an RMSD of 7.8 kcal/mol to that of the ab initio calculations. Testing has shown that the parameters are transferable and capable of reproducing the gas-phase conformations of inorganic diphosphate and triphosphate. Also, the parameters are an improvement over existing parameters in the condensed phase as shown by minimizations of ATP bound in several proteins. These parameters are intended for use with the existing AMBER 94/99 force field, and they will permit users to apply AMBER to a wider variety of important enzymatic systems. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1016–1025, 2003Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/34696/1/10262_ftp.pd

Functional interplay between NTP leaving group and base pair recognition during RNA polymerase II nucleotide incorporation revealed by methylene substitution.

RNA polymerase II (pol II) utilizes a complex interaction network to select and incorporate correct nucleoside triphosphate (NTP) substrates with high efficiency and fidelity. Our previous 'synthetic nucleic acid substitution' strategy has been successfully applied in dissecting the function of nucleic acid moieties in pol II transcription. However, how the triphosphate moiety of substrate influences the rate of P-O bond cleavage and formation during nucleotide incorporation is still unclear. Here, by employing β,γ-bridging atom-'substituted' NTPs, we elucidate how the methylene substitution in the pyrophosphate leaving group affects cognate and non-cognate nucleotide incorporation. Intriguingly, the effect of the β,γ-methylene substitution on the non-cognate UTP/dT scaffold (∼3-fold decrease in kpol) is significantly different from that of the cognate ATP/dT scaffold (∼130-fold decrease in kpol). Removal of the wobble hydrogen bonds in U:dT recovers a strong response to methylene substitution of UTP. Our kinetic and modeling studies are consistent with a unique altered transition state for bond formation and cleavage for UTP/dT incorporation compared with ATP/dT incorporation. Collectively, our data reveals the functional interplay between NTP triphosphate moiety and base pair hydrogen bonding recognition during nucleotide incorporation

ATP-magnesium coordination: Protein structure-based force field evaluation and corrections

In the numerous molecular recognition and catalytic processes across biochemistry involving adenosine triphosphate (ATP), the common bioactive form is its magnesium chelate, ATP·Mg2+. In aqueous solution, two chelation geometries predominate, distinguished by bidentate and tridentate Mg2+–phosphate coordination. These are approximately isoenergetic but separated by a high energy barrier. Force field-based atomistic simulation studies of this complex require an accurate representation of its structure and energetics. Here we focused on the energetics of ATP·Mg2+ coordination. Applying an enhanced sampling scheme to circumvent prohibitively slow sampling of transitions between coordination modes, we observed striking contradictions between Amber and CHARMM force field descriptions, most prominently in opposing predictions of the favored coordination mode. Through further configurational free energy calculations, conducted against a diverse set of ATP·Mg2+–protein complex structures to supplement otherwise limited experimental data, we quantified systematic biases for each force field. The force field calculations were strongly predictive of experimentally observed coordination modes, enabling additive corrections to the coordination free energy that deliver close agreement with experiment. We reassessed the applicability of the thus corrected force field descriptions of ATP·Mg2+ for biomolecular simulation and observed that, while the CHARMM parameters display an erroneous preference for overextended triphosphate configurations that will affect many common biomolecular simulation applications involving ATP, the force field energy landscapes broadly agree with experimental measurements of solution geometry and the distribution of ATP·Mg2+ structures found in the Protein Data Bank. Our force field evaluation and correction approach, based on maximizing consistency with the large and heterogeneous collection of structural information encoded in the PDB, should be broadly applicable to many other systems

Structural Insights into the HWE Histidine Kinase Family: The Brucella Blue Light-Activated Histidine Kinase Domain

In response to light, as part of a two-component system, the Brucella blue light-activated histidine kinase (LOV-HK) increases its autophosphorylation, modulating the virulence of this microorganism. The Brucella histidine kinase (HK) domain belongs to the HWE family, for which there is no structural information. The HWE family is exclusively present in proteobacteria and usually coupled to a wide diversity of light sensor domains. This work reports the crystal structure of the Brucella HK domain, which presents two different dimeric assemblies in the asymmetric unit: one similar to the already described canonical parallel homodimers (C) and the other, an antiparallel non-canonical (NC) dimer, each with distinct relative subdomain orientations and dimerization interfaces. Contrary to these crystallographic structures and unlike other HKs, in solution, the Brucella HK domain is monomeric and still active, showing an astonishing instability of the dimeric interface. Despite this instability, using cross-linking experiments, we show that the C dimer is the functionally relevant species. Mutational analysis demonstrates that the autophosphorylation activity occurs in cis. The different relative subdomain orientations observed for the NC and C states highlight the large conformational flexibility of the HK domain. Through the analysis of these alternative conformations by means of molecular dynamics simulations, we also propose a catalytic mechanism for Brucella LOV-HK.Fil: Rinaldi, Jimena Julieta. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Arrar, Mehrnoosh. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; ArgentinaFil: Sycz, Gabriela. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Cerutti, Maria Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina. Plataforma Argentina de Biología Estructural y Metabolómica PLABEM; ArgentinaFil: Berguer, Paula Mercedes. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Paris, Gastón. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Estrin, Dario Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; ArgentinaFil: Marti, Marcelo Adrian. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Klinke, Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina. Plataforma Argentina de Biología Estructural y Metabolómica PLABEM; ArgentinaFil: Goldbaum, Fernando Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina. Plataforma Argentina de Biología Estructural y Metabolómica PLABEM; Argentin

ATP and its N6-substituted analogues: parameterization, molecular dynamics simulation and conformational analysis

In this work we used a combination of classical molecular dynamics and simulated annealing techniques to shed more light on the conformational flexibility of 12 adenosine triphosphate (ATP) analogues in a water environment. We present simulations in AMBER force field for ATP and 12 published analogues [Shah et al. (1997) Proc Natl Acad Sci USA 94: 3565–3570]. The calculations were carried out using the generalized Born (GB) solvation model in the presence of the cation Mg2+. The ion was placed at a close distance (2 Å) from the charged oxygen atoms of the beta and gamma phosphate groups of the −3 negatively charged ATP analogue molecules. Analysis of the results revealed the distribution of inter-proton distances H8–H1′ and H8–H2′ versus the torsion angle ψ (C4–N9-C1′–O4′) for all conformations of ATP analogues. There are two gaps in the distribution of torsion angle ψ values: the first is between −30 and 30 degrees and is described by cis-conformation; and the second is between 90 and 175 degrees, which mostly covers a region of anti conformation. Our results compare favorably with results obtained in experimental assays [Jiang and Mao (2002) Polyhedron 21:435–438]

Concepts, perspectives and implications of a hybrid system made of nucleic acids biopolymers and hydroxyapatite mineral

The origin of building blocks of life and how life thrived on Earth remains a topic of high interest for researchers of the Origin of Life. In this thesis, we deal with concepts, perspectives and implications of the system termed hydroxyolite, a combination of outstanding biopolymers (nucleic acids such as DNA and RNA) and an exceptional mineral (hydroxyapatite). First we study, based on Revilla et al. (2013) and Bertran et al. (2014), how hydroxyapatite forms crystals able to encapsulate DNA or RNA when nucleic acids are used as a nucleating template. Later, in Bertran et al., (2016), we reported the mechanism of how the encapsulated nucleic acid is released to the surroundings when environmental conditions change, for instance becoming more acidic. As a consequence, we postulated that DNA existing in cells can be encapsulated and protected by hydroxyapatite against environmental attacks (i.e. poisonous gases, gamma radiation or enzymatic degradation) until they change, making feasible the reintroduction of nucleic acids in the mainstream of life. We hypothesized about the implications of such a system in the early history of life when mass extinction events occurred on Earth (Turon et al., 2015). Moreover, we extended the hydroxyolite concept, borrowed from the materials chemistry, to other disciplines such as paleontology, biology, biotechnology and medicine by considering hydroxyolites as equivalents to non-viral vectors that can introduce and release DNA into a cell (transfection). Such nucleic acid triggers the expression of foreign proteins if released in the cytosol or might be recombined with cell genome when DNA is released in the target cell nucleus. In the second part of the thesis, we studied the hydroxyolite system from a complementary perspective. We speculate about the consequences of being hydroxyapatite the first actor and not the nucleic acid. We propose that hydroxyapatite might act as an inorganic mold if considered as a catalytic substrate that facilitates the synthesis of simple organic molecules as the building blocks of life. Thus, we identified a prebiotic scenario, a volcanic eruption under lightning, where a phenomenon known as dirty storm usually occurs under certain conditions. Hydroxyapatite is known in nature to be part of igneous rocks and volcanic ash in small but significant concentrations. We replicated in the laboratory such extreme conditions by developing a thermally and electrically stimulated polarization. A process performed at 1000 ºC and under a difference of potential of 300 kV·m-1, to obtain permanently polarized hydroxyapatite (Turon et al., 2016; PCT/EP2017/069437) that turned out to be an enhanced catalyst compared to hydroxyapatite able to fix nitrogen and carbon from a gas mixture of N2, CO2 and CH4 (Rivas et al., 2018). The catalyst, under UV light, converts them into amino acids (Glycine and D/L-Alanine) and small organic molecules by means of a new inorganic photosynthetic process. In this work, we develop an integrative prebiotic model that describes how simple molecules might be synthesized from mildly reducing atmospheres by combining previous models such as volcanos as giant reactors, minerals as catalysts and photochemical reactions in the atmosphere under prebiotic sun light. All of them under the framework of a prebiotic inorganic photosynthesis, a process that might be considered the corner stone of the rise of the building blocks of life.L’origen de les molècules que van donar lloc a la vida i com la vida va prosperar a la Terra segueix essent un tema del màxim interès pels investigadors de l’origen de la vida. En aquesta tesi, discutim conceptes, perspectives de futur i implicacions del sistema que hem anomenat hidroxiolita (hydroxyolite), una combinació de biopolímers amb característiques molt especials (àcids nucleics com l’ADN i l’ARN) i un mineral excepcional (hidroxiapatita). En primer lloc, en els treballs Revilla et al., (2013) i Bertran et al., (2014) estudiem com els cristalls d’hidroxiapatita tenen la capacitat d’encapsular ADN o ARN quan l’àcid nucleic es comporta com agent nucleant. Reportem com l’àcid nucleic prèviament encapsulat pot ser alliberat si les condicions ambientals canvien, per exemple tornant-se lleugerament més àcides (Bertran et al., 2016). Com a conseqüència, postulem que l’ADN existent a les cèl·lules pot ser encapsulat per la hidroxiapatita protegint-lo contra atacs de l’entorn (per exemple, la influència de gasos tòxics, la radiació gamma o la degradació enzimàtica) fins que les condicions externes canvien i els àcids nucleics poder ser reintroduïts en el torrent principal de la vida. Discutim les implicacions d’aquest sistema híbrid a la història primitiva de la vida a la Terra, quan van ocórrer les grans catàstrofes que van donar lloc a extincions massives d’éssers vius. Tanmateix, estenem el concepte d’hidroxiolita a altres disciplines com la paleontologia, la biologia cel·lular, la biotecnologia i la medicina, considerant les hidroxiolites com a vectors no virals que poden introduir i alliberar ADN dins una cèl·lula (transfecció). Aquest àcid nucleic, si s’allibera en el citosol pot desencadenar l’expressió de proteïnes codificades en l’ADN introduït, o si s’allibera en el nucli podria recombinar-se amb el propi ADN de la cèl·lula diana de manera transitòria o permanent. A la segona part de la tesi, estudiem el sistema hidroxiolita des d’una perspectiva complementària. Especulem sobre les conseqüències de ser la hidroxiapatita l’actor principal del sistema i no l’àcid nucleic. Proposem que la hidroxiapatita pot actuar com un motlle inorgànic si es comporta com a substrat catalític que facilita la síntesi de molècules orgàniques, com les molècules que van donar lloc a la vida. A partir d’aquest concepte hem identificat un escenari prebiòtic, una erupció volcànica acompanyada de descàrregues elèctriques, fenomen que succeeix amb certa freqüència en funció de les característiques de l’erupció. La hidroxiapatita a la natura és coneguda per formar part de la composició de roques ígnies i de la cendra volcànica en petites però significatives quantitats. Al laboratori hem replicat aquestes condicions extremes i hem desenvolupat un procés de polarització mitjançant estimulació elèctrica i tèrmica, aplicant 1000 ºC i una diferència de potencial de 300 kV·m-1, que dóna com a resultat hidroxiapatita polaritzada permanentment que converteix el mineral en un catalitzador extraordinari comparat amb la hidroxiapatita i que té la capacitat de fixar nitrogen i carboni a partir d’una mescla de gasos composada per N2, CO2 i CH4 en presència d’aigua. El catalitzador, sota il·luminació de llum UV facilita la conversió d’aquests gasos en aminoàcids (Glicina i D/L-Alanina) i en molècules orgàniques simples a través d’un procés fotosintètic inorgànic. En aquest treball, desenvolupem un model prebiòtic que descriu com molècules senzilles van poder ser sintetitzades a partir d’atmosferes suaument reductores combinant models prebiòtics previs (volcans que es comporten com grans reactors, reaccions fotoquímiques que succeeixen a l’atmosfera sota el sol prebiòtic i minerals que actuen com a catalitzadors) sota el marc de la fotosíntesi inorgànica prebiòtica, un procés que podria ser considerat la pedra angular de l’aparició de les molècules que van donar lloc a la vida.El origen de las moléculas que dieron lugar a la vida y como la vida prosperó en la Tierra sigue siendo un tema del máximo interés para los investigadores del Origen de la Vida. En esta tesis discutimos conceptos, perspectivas de futuro e implicaciones del sistema que hemos denominado hidroxiolita (hydroxyolite), una combinación de biopolímeros con características muy especiales (ácidos nucleicos tales como el ADN y el ARN) y un mineral excepcional (hidroxiapatita). En primer lugar, en nuestros trabajos Revilla et al. (2013) y Bertrán et al. (2014) estudiamos como los cristales de hidroxiapatita tienen la capacidad de encapsular ADN o ARN cuando el ácido nucleico se comporta como un agente nucleante. A continuación, reportamos como el ácido nucleico previamente encapsulado puede ser liberado cuando las condiciones ambientales cambian, por ejemplo, cuando se vuelven ligeramente más ácidas (Bertrán et al., 2016). A consecuencia, postulamos que el ADN existente en las células puede ser encapsulado por la hidroxiapatita protegiéndolo contra ataques del entorno (por ejemplo, la influencia de gases tóxicos, la radiación gamma o la degradación enzimática) hasta que cambian las condiciones externas y los ácidos nucleicos pueden ser reintroducidos de nuevo en el torrente principal de la vida. A continuación, discutimos las implicaciones de este sistema híbrido en la historia primitiva de la vida en la Tierra, cuando ocurrieron las grandes catástrofes que dieron lugar a extinciones masivas de seres vivos (Turon et al., 2015). Asimismo, extendemos el concepto hidroxiolita, acuñado en la ciencia de materiales, a otras disciplinas como la paleontología, la biología celular, la biotecnología y la medicina, considerando las hidroxiolitas como vectores no virales que pueden introducir y liberar ADN dentro de una célula (transfección). Este ácido nucleico, si es liberado en el citosol puede desencadenar la expresión de proteínas codificadas en el ADN introducido, o si se libera en el núcleo podría recombinarse con el propio ADN de la célula diana de forma transitoria o permanente. En la segunda parte de la tesis, estudiamos el sistema hidroxiolita desde una perspectiva complementaria. Especulamos sobre las consecuencias de ser la hidroxiolita el actor principal y no el ácido nucleico. Proponemos que la hidroxiolita puede actuar como un molde inorgánico si se comporta como un sustrato catalítico que facilita la síntesis de moléculas orgánicas, como las moléculas que dieron lugar a la vida. Hemos identificado un escenario prebiótico basado en una erupción volcánica con descargas eléctricas, fenómeno que ocurre con cierta frecuencia en función de las características de la erupción. La hidroxiapatita es conocida en la naturaleza por formar parte de la composición de rocas ígneas y ceniza volcánica en bajas pero significativas concentraciones. Hemos replicado en el laboratorio estas condiciones extremas y hemos desarrollado un proceso de polarización mediante estimulación térmica y eléctrica, aplicando 1000ºC y una diferencia de potencial de 300 kV·m-1, que da como resultado hidroxiapatita permanentemente polarizada (Turón et al, 2016; PCT/EP2017/069437). Este proceso convierte el mineral en un catalizador extraordinario comparado con la hidroxiapatita y tiene la capacidad de fijar nitrógeno y carbono a partir de una mezcla de gases compuesta por N2, CO2 y CH4 (Rivas et al., 2018) en presencia de agua. El catalizador, bajo iluminación de luz UV, facilita la conversión de estos gases en aminoácidos (Glicina y D/L-Alanina) y en ácidos orgánicos simples a través de un proceso de fotosíntesis inorgánica. En este trabajo desarrollamos un modelo prebiótico que describe como moléculas sencillas pudieron ser sintetizadas a partir de atmósferas suavemente reductores combinando modelos prebióticos ya existentes (volcanes que se comportan grandes reactores, reacciones fotoquímicas que ocurren en la atmosfera bajo el sol prebiótico y minerales que actúan como catalizadores) bajo el marco de una fotosíntesis prebiótica inorgánica, un proceso que podría ser considerado la piedra angular en la que se basó la aparición de las moléculas que dieron lugar a la vida.Postprint (published version

Path Reweighting Methods for underdamped Langevin Dynamics for Molecular Systems

Knowledge about the dynamical properties of biomolecules is essential to understand their function in biological processes. This thesis approaches the task to compute dynamical properties with two different strategies. Part A focuses on Molecular Dynamics (MD) simulations combined with path reweighting. Three of the most widely used underdamped Langevin integrators for MD simulations are the splitting methods BAOAB and BAOA which are available in the MD packages OpenMM and AMBER and the Gromacs Stochastic Dynamics (GSD) integrator implemented in GROMACS. We found that all three integrators are equivalent configurational sampling algorithms and thus yield configurational properties at equivalent accuracy. MD simulations with stochastic integrators such as Langevin integrators offer the possibility to reweight estimated dynamical properties using path reweighting. With path reweighting we can for example recover the original dynamics from MD simulation that have been conducted with enhanced sampling methods. The key component of path reweighting is the path reweighting factor M which strongly depends on the chosen integrator. We derive M_L for underdamped Langevin dynamics propagated by a variant of the Langevin Leapfrog integrator. Additionally, we present two strategies which can be used as blueprints to straightforwardly derive M_L for other Langevin integrators. The previously reported path reweighting factor matches the Euler-Maruyama integrator for overdamped Langevin dynamics and was used as standard reweighting factor even though the MD simulation was conducted with an underdamped Langevin integrator. We prove that this path reweighting factors differs from the exact M_L only by O(ξ^4 ∆t^4) and thus yields highly accurate dynamical reweighting results (∆t is the integration time step, and ξ is the collision rate.). Part B of this thesis combines experimental and theoretical approaches to investigate Multiple Inositol Polyphosphate Phosphatase 1 (MINPP1)-mediated inositol polyphosphate (InsP) networks. We use 13C-labeling experiments combined with nuclear magnetic resonance spectroscopy (NMR) to uncover a novel branch of InsP dephosphorylation in human cells. Additionally, we extract the corresponding reaction rates using a Markovian kinetic scheme as theoretical model to describe the network

Computational Prediction of the Mode of Binding of Antitumor Lankacidin C to Tubulin

Lankacidin C, which is an antibiotic produced by the organism Streptomyces rochei, shows considerable antitumor activity. The mechanism of its antitumor activity remained elusive for decades until it was recently shown to overstabilize microtubules by binding at the taxol binding site of tubulin, causing mitotic arrest followed by apoptosis. However, the exact binding mode of lankacidin C inside the tubulin binding pocket remains unknown, an issue that impedes proper structure-based design, modification, and optimization of the drug. Here, we have used computational methods to predict the most likely binding mode of lankacidin C to tubulin. We employed ensemble-based docking in different software packages, supplemented with molecular dynamics simulation and subsequent binding-energy prediction. The molecular dynamics simulations performed on lankacidin C were collectively 1.1 μs long. Also, a multiple-trajectory approach was performed to assess the stability of different potential binding modes. The identified binding mode could serve as an ideal starting point for structural modification and optimization of lankacidin C to enhance its affinity to the tubulin binding site and therefore improve its antitumor activity.The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acsomega.8b03470