Sulfide-binding hemoglobins: Effects of mutations on active-site flexibility

The dynamics of Hemoglobin I (HbI) from the clam Lucina pectinata, from wild-type sperm whale (SW) myoglobin, and from the L29F/H64Q/V68F triple mutant of SW, both unligated and bound to hydrogen sulfide (H2S), have been studied in molecular dynamics simulations. Features that account for differences in H2S affinity among the three have been examined. Our results verify the existence of an unusual heme rocking motion in unligated HbI that can promote the entrance of large ligands such as H2S. The FQF-mutant partially reproduces the amplitude and relative orientation of the motion of HbI's heme group. Therefore, besides introducing favorable electrostatic interactions with H2S, the three mutations in the distal pocket change the dynamic properties of the heme group. The active-site residues Gln-64(E7), Phe-43(CD1), and His-93(F8) are also shown to be more flexible in unligated HbI than in FQF-mutant and SW. Further contributions to H2S affinity come from differences in hydrogen bonding between the heme propionate groups and nearby amino acid residues.Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicada

Sulfide-binding hemoglobins: Effects of mutations on active-site flexibility

The dynamics of Hemoglobin I (HbI) from the clam Lucina pectinata, from wild-type sperm whale (SW) myoglobin, and from the L29F/H64Q/V68F triple mutant of SW, both unligated and bound to hydrogen sulfide (H2S), have been studied in molecular dynamics simulations. Features that account for differences in H2S affinity among the three have been examined. Our results verify the existence of an unusual heme rocking motion in unligated HbI that can promote the entrance of large ligands such as H2S. The FQF-mutant partially reproduces the amplitude and relative orientation of the motion of HbI's heme group. Therefore, besides introducing favorable electrostatic interactions with H2S, the three mutations in the distal pocket change the dynamic properties of the heme group. The active-site residues Gln-64(E7), Phe-43(CD1), and His-93(F8) are also shown to be more flexible in unligated HbI than in FQF-mutant and SW. Further contributions to H2S affinity come from differences in hydrogen bonding between the heme propionate groups and nearby amino acid residues.Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicada

An ab initio multiple cloning approach for the simulation of photoinduced dynamics in conjugated molecules

We present a new implementation of the Ab Initio Multiple Cloning (AIMC) method, which is applied for non-adiabatic excited-state molecular dynamics simulations of photoinduced processes in conjugated molecules. Within our framework, the multidimensional wave-function is decomposed into a superposition of a number of Gaussian coherent states guided by Ehrenfest trajectories that are suited to clone and swap their electronic amplitudes throughout the simulation. New generalized cloning criteria are defined and tested. Because of sharp changes of the electronic states, which are common for conjugated polymers, the electronic parts of the Gaussian coherent states are represented in the Time Dependent Diabatic Basis (TDDB). The input to these simulations in terms of the excited-state energies, gradients and non-adiabatic couplings, is calculated on-the-fly using the Collective Electron Oscillator (CEO) approach. As a test case, we consider the photoinduced unidirectional electronic and vibrational energy transfer between two- and three-ring linear poly(phenylene ethynylene) units linked by meta-substitution. The effects of the cloning procedure on electronic and vibrational coherence, relaxation and unidirectional energy transfer between dendritic branches are discussed

Photoinduced non-adiabatic energy transfer pathways in dendrimer building blocks

The efficiency of the intramolecular energy transfer in light harvesting dendrimers is determined by their well-defined architecture with high degree of order. After photoexcitation, through-space and through-bond energy transfer mechanisms can take place, involving vectorial exciton migration among different chromophores within dendrimer highly branched structures. Their inherent intramolecular energy gradient depends on how the multiple chromophoric units have been assembled, subject to their inter-connects, spatial distances, and orientations. Herein, we compare the photoinduced nonadiabatic molecular dynamics simulations performed on a set of different combinations of a chain of linked dendrimer building blocks composed of two-, three-, and four-ring linear polyphenylene chromophoric units. The calculations are performed with the recently developed ab initio multiple cloning-time dependent diabatic basis implementation of the Multiconfigurational Ehrenfest (MCE) approach. Despite differences in short time relaxation pathways and different initial exciton localization, at longer time scales, electronic relaxation rates and exciton final redistributions are very similar for all combinations. Unlike the systems composed of two building blocks, considered previously, for the larger 3 block systems here we observe that bifurcation of the wave function accounted by cloning is important. In all the systems considered in this work, at the time scale of few hundreds of femtoseconds, cloning enhances the electronic energy relaxation by ∼13% compared to that of the MCE method without cloning. Thus, accurate description of quantum effects is essential for understanding of the energy exchange in dendrimers both at short and long time scales

Sulfide-binding hemoglobins: Effects of mutations on active-site flexibility

The dynamics of Hemoglobin I (HbI) from the clam Lucina pectinata, from wild-type sperm whale (SW) myoglobin, and from the L29F/H64Q/V68F triple mutant of SW, both unligated and bound to hydrogen sulfide (H2S), have been studied in molecular dynamics simulations. Features that account for differences in H2S affinity among the three have been examined. Our results verify the existence of an unusual heme rocking motion in unligated HbI that can promote the entrance of large ligands such as H2S. The FQF-mutant partially reproduces the amplitude and relative orientation of the motion of HbI's heme group. Therefore, besides introducing favorable electrostatic interactions with H2S, the three mutations in the distal pocket change the dynamic properties of the heme group. The active-site residues Gln-64(E7), Phe-43(CD1), and His-93(F8) are also shown to be more flexible in unligated HbI than in FQF-mutant and SW. Further contributions to H2S affinity come from differences in hydrogen bonding between the heme propionate groups and nearby amino acid residues.Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicada

Vibrational energy redistribution during donor-acceptor electronic energy transfer: criteria to identify subsets of active normal modes

Photoinduced electronic energy transfer in conjugated donor-acceptor systems is naturally accompanied by intramolecular vibrational energy redistributions accepting an excess of electronic energy. Herein, we simulate these processes in a covalently linked donor-acceptor molecular dyad system by using nonadiabatic excited state molecular dynamics simulations. We analyze different complementary criteria to systematically identify the subset of vibrational normal modes that actively participate on the donoracceptor (S2S1) electronic relaxation. We analyze energy transfer coordinates in terms ofstate-specific normal modes defined according to the different potential energy surfaces (PESs) involved. On one hand, we identify those vibrations that contribute the most to the direction of the main driving force on the nuclei during electronic transitions, represented by the non-adiabatic derivative coupling vector between donor and acceptor electronic states. On the other hand, we monitor normal mode transient accumulations of excess energy and their intramolecular energy redistribution fluxes. We observe that the subset of active modes varies according to the PES on which they belong and these modes experience the most significant rearrangements and mixing. Whereas the nuclear motions that promote donoracceptor energy funneling can be localized mainly on one or two normal modes of the S2 state, they become spread out across multiple normal modes of the S1 state following the energy transfer eventThis work was partially supported by CONICET, UNQ, ANPCyT (PICT-2018-2360), the Universidad Carlos III de Madrid, the European Union’s Seventh Framework Programme for research, technological development and demonstration under grant agreement No. 600371, el Ministerio de Economía, Industria y Competitividad (COFUND2014-51509), el Ministerio de Educación, cultura y Deporte (CEI-15-17), Banco Santander and el Ministerio de Ciencia, Innovación y Universidades (RTI2018-101020-B-I00). We also acknowledge support from the Bavarian University Centre for Latin America (BAYLAT). The work at Los Alamos National Laboratory (LANL) was supported by the Laboratory Directed Research and Development Funds (LDRD) program. This work was done in part at the Center for Nonlinear Studies (CNLS) and the Center for Integrated Nanotechnologies (CINT), a U.S. Department of Energy and Office of Basic Energy Sciences user facility, at LANL. This research used resources provided by the LANL Institutional Computing Program. Los Alamos National Laboratory is operated by Triad National Security, LLC, for the National Nuclear Security Administration of the U.S. Department of Energy. This work has received finantial support provided by the Spanish Agencia Estatal de Investigación (AEI) and Fondo Europeo de Desarrollo Regional (FEDER, UE) under Project CTQ2016-79345-P and by the Funda-ción Séneca under Project 20789/PI/18

Mechanisms of light energy harvesting in dendrimers and hyperbranched polymers

Since their earliest synthesis, much interest has arisen in the use of dendritic and structurally allied forms of polymer for light energy harvesting, especially as organic adjuncts for solar energy devices. With the facility to accommodate a proliferation of antenna chromophores, such materials can capture and channel light energy with a high degree of efficiency, each polymer unit potentially delivering the energy of one photon-or more, when optical nonlinearity is involved. To ensure the highest efficiency of operation, it is essential to understand the processes responsible for photon capture and channelling of the resulting electronic excitation. Highlighting the latest theoretical advances, this paper reviews the principal mechanisms, which prove to involve a complex interplay of structural, spectroscopic and electrodynamic properties. Designing materials with the capacity to capture and control light energy facilitates applications that now extend from solar energy to medical photonics. © 2011 by the authors; licensee MDPI, Basel, Switzerland

Reverse engineering synthetic antiviral amyloids

Human amyloids have been shown to interact with viruses and interfere with viral replication. Based on this observation, we employed a synthetic biology approach in which we engineered virus-specific amyloids against influenza A and Zika proteins. Each amyloid shares a homologous aggregation-prone fragment with a specific viral target protein. For influenza we demonstrate that a designer amyloid against PB2 accumulates in influenza A-infected tissue in vivo. Moreover, this amyloid acts specifically against influenza A and its common PB2 polymorphisms, but not influenza B, which lacks the homologous fragment. Our model amyloid demonstrates that the sequence specificity of amyloid interactions has the capacity to tune amyloid-virus interactions while allowing for the flexibility to maintain activity on evolutionary diverging variants. Some human amyloid proteins have been shown to interact with viral proteins, suggesting that they may have potential as therapeutic agents. Here the authors design synthetic amyloids specific for influenza A and Zika virus proteins, respectively, and show that they can inhibit viral replication

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009-2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world's planktonic ecosystems