Molecular dynamics simulations in photosynthesis

Photosynthesis is regulated by a dynamic interplay between proteins, enzymes, pigments, lipids, and cofactors that takes place on a large spatio-temporal scale. Molecular dynamics (MD) simulations provide a powerful toolkit to investigate dynamical processes in (bio)molecular ensembles from the (sub)picosecond to the (sub)millisecond regime and from the Å to hundreds of nm length scale. Therefore, MD is well suited to address a variety of questions arising in the field of photosynthesis research. In this review, we provide an introduction to the basic concepts of MD simulations, at atomistic and coarse-grained level of resolution. Furthermore, we discuss applications of MD simulations to model photosynthetic systems of different sizes and complexity and their connection to experimental observables. Finally, we provide a brief glance on which methods provide opportunities to capture phenomena beyond the applicability of classical MD

Role of quantum chemical calculations in molecular biophysics with a historical perspective

We discuss how the basic principles of quantum chemistry and quantum mechanics can be and have been applied to a variety of problems in molecular biophysics. First, the historical development of quantum concepts in biophysics is discussed. Next, we describe a series of interesting applications of quantum chemical methods for studying biologically active molecules, molecular structures, and some of the important processes which play a role in living organisms. We discuss the application of quantum chemistry to such processes as energy storage and transformation, and the transmission of genetic information. Quantum chemical approaches are essential to comprehend and understand the molecular nature of these processes. To conclude our work, we present a short discussion of the perspectives of quantum chemical methods in modern biophysics, the field of experimental and theoretical chiral vibrational and electronic spectroscopy

Vibrational Properties of Quinones in Photosynthetic Reaction Centers

Fourier transform infrared difference spectroscopy (FTIR DS) is widely used to study the structural details of electron transfer cofactors in photosynthetic protein complexes. In photosynthetic proteins quinones play an important role, functioning as a cofactor in light-driven electron transfer. In photosystem I (PS I) phylloquinone (PhQ) functions as an intermediary in electron transfer. To investigate the properties of PhQ that occupies the, so called, A1 binding site in PS I, time-resolved step-scan FTIR DS, with 5µs time resolution at 77K has been used. By replacing PhQ in the A1 binding site with specifically isotope labeled version, information on the vibrational frequencies associated specifically with the quinone in the binding site were obtained, which could be compared to the vibrational properties of quinone in solution or quinones in other protein binding sites. To further aid in assessing the origin of bands in the spectra, quantum mechanics /molecular mechanics (QM/MM) ONIOM type calculations were undertaken. ONIOM is an acronym for Our own N-layered Integrated molecular Orbital and molecular Mechanics. We find that the phytyl tail of PhQ does not play an important role in the orientation of PhQ in the A1 binding site. We also find that PhQ, in both neutral and reduced states, is strongly hydrogen bonded. To test and verify the applicability of our QM/MM approach, ONIOM calculations were also undertaken for ubiquinone and a variety of other quinones incorporated into the, so called, QA binding site in purple bacteria photosynthetic reaction centers. The calculated and experimental spectra agree well, demonstrating the utility and applicability of our ONIOM approach. Hydrogen bonding to the carbonyl groups of quinones in the QA binding site was shown to be relatively weak, and it was found that hydrogen bonding to neutral ubiquinone in purple bacterial reaction centers can be considered in purely electrostatic terms, contrary to the widely held belief that the hydrogen bonding amino acids should be treated quantum mechanically

Atomistic study of the long-lived quantum coherences in the Fenna-Matthews-Olson complex

A remarkable amount of theoretical research has been carried out to elucidate the physical origins of the recently observed long-lived quantum coherence in the electronic energy transfer process in biological photosynthetic systems. Although successful in many respects, several widely used descriptions only include an effective treatment of the protein-chromophore interactions. In this work, by combining an all-atom molecular dynamics simulation, time-dependent density functional theory, and open quantum system approaches, we successfully simulate the dynamics of the electronic energy transfer of the Fenna-Matthews-Olson pigment-protein complex. The resulting characteristic beating of populations and quantum coherences is in good agreement with the experimental results and the hierarchy equation of motion approach. The experimental absorption, linear and circular dichroism spectra and dephasing rates are recovered at two different temperatures. In addition, we provide an extension of our method to include zero-point fluctuations of the vibrational environment. This work thus presents one of the first steps to explain the role of excitonic quantum coherence in photosynthetic light-harvesting complexes based on their atomistic and molecular description.Comment: 24 pages, 6 figure

Successes & challenges in the atomistic modeling of light-harvesting and its photoregulation

Light-harvesting is a crucial step of photosynthesis. Its mechanisms and related energetics have been revealed by a combination of experimental investigations and theoretical modeling. The success of theoretical modeling is largely due to the application of atomistic descriptions combining quantum chemistry, classical models and molecular dynamics techniques. Besides the important achievements obtained so far, a complete and quantitative understanding of how the many different light-harvesting complexes exploit their structural specificity is still missing. Moreover, many questions remain unanswered regarding the mechanisms through which light-harvesting is regulated in response to variable light conditions. Here we show that, in both fields, a major role will be played once more by atomistic descriptions, possibly generalized to tackle the numerous time and space scales on which the regulation takes place: going from the ultrafast electronic excitation of the multichromophoric aggregate, through the subsequent conformational changes in the embedding protein, up to the interaction between proteins

Coherent dynamics in solar energy transduction

This thesis is concerned with the transfer of energy from light to matter. Over a century ago it was established that light consists of packets of energy [1], now known as photons. Not much later the energy levels of matter at the atomic scale were found to be discrete [2]. These phenomena required a new physical description that has become the theory of quantum mechanics [3]. Now, this theory of light and matter could contribute to tackling a fundamental socioeconomic and technological challenge: To find a sustainable supply of useful energy that is cheap, abundant and generated on-the-spotUBL - phd migration 201

New computational methods for structural modeling protein-protein and protein-nucleic acid interactions

Programa de Doctorat en Biomedicina[eng] The study of the 3D structural details of protein-protein and protein-DNA interactions is essential to understand biomolecular functions at the molecular level. Given the difficulty of the structural determination of these complexes by experimental techniques, computational tools are becoming a powerful to increase the actual structural coverage of protein-protein and protein-DNA interactions. pyDock is one of these tools, which uses its scoring function to determine the quality of models generated by other tools. pyDock is usually combined with the model sampling methods FTDOCK or ZDOCK. This combination has shown a consistently good prediction performance in community-wide assessment experiments like CAPRI or CASP and has provided biological insights and insightful interpretation of experiments by modeling many biomolecular interactions of biomedical and biotechnological interest. This software combination has demonstrated good predictive performance in the blinded evaluation experiments CAPRI and CASP. It has provided biological insights by modeling many biomolecular interactions of biomedical and biotechnological interest. Here, we describe a pyDock software update, which includes its adaptation to the newest python code, the capability of including cofactor and other small molecules, and an internal parallelization to use the computational resources more efficiently. A strategy was designed to integrate the template-based docking and ab initio docking approaches by creating a new scoring function based on the pyDock scoring energy basis function and the TM-score measure of structural similarity of protein structures. This strategy was partially used for our participation in the 7th CAPRI, the 3rd CASP-CAPRI and the 4th CASP-CAPRI joint experiments. These experiments were challenging, as we needed to model protein-protein complexes, multimeric oligomerization proteins, protein-peptide, and protein-oligosaccharide interactions. Many proposed targets required the efficient integration of rigid-body docking, template-based modeling, flexible optimization, multi- parametric scoring, and experimental restraints. This was especially relevant for the multi- molecular assemblies proposed in the 3er and 4th CASP-CAPRI joint experiments. In addition, a case study, in which electron transfer protein complexes were modelled to test the software new capabilities. Good results were achieved as the structural models obtained help explaining the differences in photosynthetic efficiency between red and green algae

Single molecule electrochemical studies of photosynthetic complexes

[eng] In this thesis manuscript entitled “Single molecule electrochemical studies of photosynthetic complexes” I study the Photosystem I (PSI) protein complex to characterize fundamental processes of the PSI function. PSI is a light harvesting complex located in the thylakoid membrane of algae and plants that pumps electrons throughout this membrane. Upon irradiation, PSI oxidizes plastocyanin (Pc) and reduces ferredoxin (Fd), that is, PSI is a light-driven oxidoreductase. In this dissertation, experimental results are presented regarding: i) The protein electron transfer and protein electron transport within the complex ii) The interprotein electron transfer with plastocyanin iii) The binding with plastocyanin and the influence of photosystem and plastocyanin redox state on their association iv) The excitonic-energy transfer within the light harvesting antenna of the photosystem. The novelty of the results presented here lies on the experimental approach. For this thesis, I have developed single protein techniques allowing to study single PSI, and single PSI-Pc pairs making use of nanoprobes techniques, electrochemical scanning tunnelling microscopy and spectroscopy (EC- STM and EC-TS) and atomic force microscopy and single molecule force spectroscopy (AFM, SMFS). This have been achieved optimizing the binding of PSI and Pc to gold electrodes and nanoprobes allowing to orient and face the interacting complexes. In particular I have studied the charge exchange distance of PSI and PSI-Pc complexes by tunnel current distance decay spectroscopy. I have observed, in line with previous results of the group, that proteins pairs are able to exchange charge up to several nanometers distance. I have also studied the conductance of the PSI-Pc complex. For both experiments, we have observed that Pc devoid of its Cu redox center is able to transfer charge at longer distances and with higher conductances with respect to the holo form incorporating Cu2+. I have also observed that the binding probability of the PSI-Pc complex is modulated by the redox state of the proteins. In collaboration with my colleagues we have developed a methodology to control orthogonally the redox state of PSI (with light) and Pc (with specific reducing agent). We have observed that the binding probability is enhanced when at least one of the complex is in an ET ready (PSI oxidized, Pc reduced) state. To study the excitonic energy transfer in PSI antennae, we have developed in collaboration with the institute of photonic sciences a novel photocurrent detected spectroscopic technique. We measure the electrochemical current signal, proportional to the population of charge separated states as the sample is exposed to pulsed-laser irradiation. The optical set-up consists on a fully collinear, action detected (photocurrent) two-dimensional spectroscopy. In addition, making use of PSI functionalized electrodes, I have explored the feasibility of a photocurrent-based herbicide biosensor. The photocurrent output and kinetics were systematically studied and modelled. Altogether, I hope that the works presented in this manuscript contribute to the understanding of the electron transfer in proteins and in particular for the photosystem I complex.[spa] En esta tesis estudio la transferencia de electrones entre proteínas usando como modelos el fotosistema I y su pareja donadora de electrones en la fotosíntesis, la plastocianina. He medido dos etapas del proceso de transferencia electrónica, la asociación/disociación del complejo que forman y el intercambio de electrones entre el par. He caracterizado estos procesos en proteínas individuales empleando nano-microscopia y espectroscopía de sonda próxima, en concreto microscopía de fuerza atómica para el estudio de la asociación/disociación y microscopía scanner de efecto túnel en medio electroquímico en los experimentos de intercambio electrónico. Para ambos estudios, he expresado mutantes de plastocianina y he desarrollado péptidos de anclaje al fotosistema I para orientar al par de proteínas sobre electrodos de oro. Los experimentos de espectroscopía de fuerza revelan que la probabilidad de asociación entre el par de proteínas está modulada por su estado redox. En concreto, he observado que, si al menos una de las dos proteínas esté preparada para intercambiar carga, es decir si el fotosistema está oxidado o la plastocianina reducida, la probabilidad de asociación es mayor que la que observamos en el sistema fotosistema reducido y plastocianina oxidada. En el caso del intercambio electrónico, he estudiado el fotosistema I aislado, así como el par fotosistema plastocianina. En ambos casos observamos que el fotosistema es capaz de intercambiar electrones a varios nanómetros de distancia a través del electrolito con la sonda desnuda y con la sonda decorada con plastocianina respectivamente. También he estudiado el efecto del centro redox de cobre de la plastocianina en la conductancia y distancia de intercambio electrónico. Paralelamente, he explotado la fotocorriente que produce el fotosistema en dos pruebas de concepto, de carácter fundamental y aplicado, aprovechando las herramientas empleadas para medir la transferencia electrónica en el fotosistema I. Por un lado, hemos desarrollado junto con el Instituto de Ciencias Fotónicas y la universidad de Padova, un sistema de detección de fotocorriente electroquímica como observable en experimentos de espectroscopía electrónica de dos dimensiones. En la vertiente aplicada, hemos empleado la fotocorriente para determinar la concentración de un herbicida (paraquat)