Molecular Modeling in Enzyme Design, Toward In Silico Guided Directed Evolution

Directed evolution (DE) creates diversity in subsequent rounds of mutagenesis in the quest of increased protein stability, substrate binding, and catalysis. Although this technique does not require any structural/mechanistic knowledge of the system, the frequency of improved mutations is usually low. For this reason, computational tools are increasingly used to focus the search in sequence space, enhancing the efficiency of laboratory evolution. In particular, molecular modeling methods provide a unique tool to grasp the sequence/structure/function relationship of the protein to evolve, with the only condition that a structural model is provided. With this book chapter, we tried to guide the reader through the state of the art of molecular modeling, discussing their strengths, limitations, and directions. In addition, we suggest a possible future template for in silico directed evolution where we underline two main points: a hierarchical computational protocol combining several different techniques and a synergic effort between simulations and experimental validation.Peer ReviewedPostprint (author's final draft

Ecoupling server: A tool to compute and analyze electronic couplings

Electron transfer processes are often studied through the evaluation and analysis of the electronic coupling (EC). Since most standard QM codes do not provide readily such a measure, additional, and user-friendly tools to compute and analyze electronic coupling from external wave functions will be of high value. The first server to provide a friendly interface for evaluation and analysis of electronic couplings under two different approximations (FDC and GMH) is presented in this communication. Ecoupling server accepts inputs from common QM and QM/MM software and provides useful plots to understand and analyze the results easily. The web server has been implemented in CGI-python using Apache and it is accessible at http://ecouplingserver.bsc.es. Ecoupling server is free and open to all users without login.This work has been funded by the Spanish Ministry of Education and Science through the Project CTQ2013-48287.Peer ReviewedPostprint (author's final draft

Computer-aided laccase engineering: toward biological oxidation of arylamines

Oxidation of arylamines, such as aniline, is of high industrial interest and laccases have been proposed as biocata-lysts to replace harsh chemical oxidants. However, the reaction is hampered by the redox potential of the substrate at acid pH and enzyme engineering is required to improve the oxidation. In this work, instead of trying to improve the redox potential of the en-zyme, we aim towards the (transient) substrate’s one and propose this as a more reliable strategy. We have successfully combined a computational approach with experimental validation to rationally design an improved biocatalyst. The in silico protocol combines classical and quantum mechanics to deliver atomic and electronic level detail on the two main processes involved: substrate binding and electron transfer. After mutant expression and comparison to the parent type, kinetic results show that the protocol accurately predicts aniline’s improved oxidation (2-fold kcat increase) in the engineered variant for biocatalyzed polyaniline production.This study was supported by the INDOX (KBBE-2013-7-613549) EU-project, and the NOESIS (BI0201456388-R) and OxiDesign (CTQ2013-48287-R) Spanish project. GS thanks an FPI grant of the Spanish Ministry of Competitiveness.Peer ReviewedPostprint (author's final draft

Rational Enzyme Engineering Through Biophysical and Biochemical Modeling

Due to its importance in the pharmaceutical industry, ligand dynamic simulations have experienced a great expansion. Using all-atom models and cutting edge hardware, one can perform non-biased ligand migration, active site search and binding studies. In this letter we demonstrate (and validate by PCR mutagenesis) how these techniques, when combined with quantum mechanics, open new possibilities in enzyme engineering. We provide a complete analysis where: 1) biophysical simulations produce ligand diffusion and, 2) biochemical modeling samples the chemical event. Using such broad analysis we engineer a highly stable peroxidase activating the enzyme for new substrate oxidation after rational mutation of two non-conserved surface residues. In particular, we create a new surface-binding site, quantitatively predicting the in vitro change in oxidation rate obtained by mutagenic PCR and achieving a comparable specificity constant to active peroxidases.This work was supported by the INDOX (KBBE-2013-7-613549 to ATM) European project, and the CTQ2013-48287 (to VG) and BIO2014-56388-R (to FJR-D) projects of the Spanish Ministry of Economy and Competitiveness (MINECO). FJR-D acknowledges a MINECO Ramón&Cajal contract.Peer ReviewedPostprint (author's final draft

Improving the Oxidative Stability of a High Redox Potential Fungal Peroxidase by Rational Design

Ligninolytic peroxidases are enzymes of biotechnological interest due to their ability to oxidize high redox potential aromatic compounds, including the recalcitrant lignin polymer. However, different obstacles prevent their use in industrial and environmental applications, including low stability towards their natural oxidizing-substrate H2O2. In this work, versatile peroxidase was taken as a model ligninolytic peroxidase, its oxidative inactivation by H2O2 was studied and different strategies were evaluated with the aim of improving H2O2 stability. Oxidation of the methionine residues was produced during enzyme inactivation by H2O2 excess. Substitution of these residues, located near the heme cofactor and the catalytic tryptophan, rendered a variant with a 7.8-fold decreased oxidative inactivation rate. A second strategy consisted in mutating two residues (Thr45 and Ile103) near the catalytic distal histidine with the aim of modifying the reactivity of the enzyme with H2O2. The T45A/I103T variant showed a 2.9-fold slower reaction rate with H2O2 and 2.8-fold enhanced oxidative stability. Finally, both strategies were combined in the T45A/I103T/M152F/M262F/M265L variant, whose stability in the presence of H2O2 was improved 11.7-fold. This variant showed an increased half-life, over 30 min compared with 3.4 min of the native enzyme, under an excess of 2000 equivalents of H2O2. Interestingly, the stability improvement achieved was related with slower formation, subsequent stabilization and slower bleaching of the enzyme Compound III, a peroxidase intermediate that is not part of the catalytic cycle and leads to the inactivation of the enzyme.This work was funded by the Commission of the European Communities through the INDOX project (KBBE-2013-7-613549, "Optimized oxidoreductases for medium and large scale industrial biotransformations"), and by the Spanish Ministerio de Economía y Competitividad (MINECO) through the HIPOP project (BIO2011-26694, “Screening and engineering of new high-redoxpotential peroxidases”). VS-J and FJR-D thank the financial support of a research fellowship (Formación de Personal Investigador, FPI) and a Ramón y Cajal contract of the Spanish MINECO, respectively. The authors have no conflict of interest to declare. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer ReviewedPostprint (published version

A Neutrophil Timer Coordinates Immune Defense and Vascular Protection

Neutrophils eliminate pathogens efficiently but can inflict severe damage to the host if they over-activate within blood vessels. It is unclear how immunity solves the dilemma of mounting an efficient anti-microbial defense while preserving vascular health. Here, we identify a neutrophil-intrinsic program that enabled both. The gene Bmal1 regulated expression of the chemokine CXCL2 to induce chemokine receptor CXCR2-dependent diurnal changes in the transcriptional and migratory properties of circulating neutrophils. These diurnal alterations, referred to as neutrophil aging, were antagonized by CXCR4 (C-X-C chemokine receptor type 4) and regulated the outer topology of neutrophils to favor homeostatic egress from blood vessels at night, resulting in boosted anti-microbial activity in tissues. Mice engineered for constitutive neutrophil aging became resistant to infection, but the persistence of intravascular aged neutrophils predisposed them to thrombo-inflammation and death. Thus, diurnal compartmentalization of neutrophils, driven by an internal timer, coordinates immune defense and vascular protection. Neutrophils display circadian oscillations in numbers and phenotype in the circulation. Adrover and colleagues now identify the molecular regulators of neutrophil aging and show that genetic disruption of this process has major consequences in immune cell trafficking, anti-microbial defense, and vascular health.This study was supported by Intramural grants from A∗STAR to L.G.N., BES-2013-065550 to J.M.A., BES-2010-032828 to M.C.-A, and JCI-2012-14147 to L.A.W (all from Ministerio de Economía, Industria y Competitividad; MEIC). Additional MEIC grants were SAF2014-61993-EXP to C.L.-R.; SAF2015-68632-R to M.A.M. and SAF-2013-42920R and SAF2016-79040Rto D.S. D.S. also received 635122-PROCROP H2020 from the European Commission and ERC CoG 725091 from the European Research Council (ERC). ERC AdG 692511 PROVASC from the ERC and SFB1123-A1 from the Deutsche Forschungsgemeinschaft were given to C.W.; MHA VD1.2/81Z1600212 from the German Center for Cardiovascular Research (DZHK) was given to C.W. and O.S.; SFB1123-A6 was given to O.S.; SFB914-B08 was given to O.S. and C.W.; and INST 211/604-2, ZA 428/12-1, and ZA 428/13-1 were given to A.Z. This study was also supported by PI12/00494 from Fondo de Investigaciones Sanitarias (FIS) to C.M.; PI13/01979, Cardiovascular Network grant RD 12/0042/0054, and CIBERCV to B.I.; SAF2015-65607-R, SAF2013-49662-EXP, and PCIN-2014-103 from MEIC; and co-funding by Fondo Europeo de Desarrollo Regional (FEDER) to A.H. The CNIC is supported by the MEIC and the Pro CNIC Foundation and is a Severo Ochoa Center of Excellence (MEIC award SEV-2015-0505)

A Neutrophil Timer Coordinates Immune Defense and Vascular Protection

Neutrophils eliminate pathogens efficiently but can inflict severe damage to the host if they over-activate within blood vessels. It is unclear how immunity solves the dilemma of mounting an efficient anti-microbial defense while preserving vascular health. Here, we identify a neutrophil-intrinsic program that enabled both. The gene Bmal1 regulated expression of the chemokine CXCL2 to induce chemokine receptor CXCR2-dependent diurnal changes in the transcriptional and migratory properties of circulating neutrophils. These diurnal alterations, referred to as neutrophil aging, were antagonized by CXCR4 (C-X-C chemokine receptor type 4) and regulated the outer topology of neutrophils to favor homeostatic egress from blood vessels at night, resulting in boosted anti-microbial activity in tissues. Mice engineered for constitutive neutrophil aging became resistant to infection, but the persistence of intravascular aged neutrophils predisposed them to thrombo-inflammation and death. Thus, diurnal compartmentalization of neutrophils, driven by an internal timer, coordinates immune defense and vascular protection.We thank all members of the Hidalgo Lab for discussion and insightful comments; J.M. Ligos, R. Nieto, and M. Viton for help with sorting and cytometric analyses; I. Ortega and E. Santos for animal husbandry; D. Rico, M.J. Gomez, C. Torroja, and F. Sanchez-Cabo for insightful comments and help with transcriptomic analyses; V. Labrador, E. Arza, A.M. Santos, and the Microscopy Unit of the CNIC for help with microscopy; S. Aznar-Benitah, U. Albrecht, Q.-J. Meng, B. Staels, and H. Duez for the generous gift of mice; J.A. Enriquez and J. Avila for scientific insights; and J.M. Garcia and A. Diez de la Cortina for art. This study was supported by Intramural grants from A* STAR to L.G.N., BES-2013-065550 to J.M.A., BES-2010-032828 to M.C.-A, and JCI-2012-14147 to L.A.W (all from Ministerio de Economia, Industria y Competitividad; MEIC). Additional MEIC grants were SAF2014-61993-EXP to C.L.-R.; SAF2015-68632-R to M.A.M. and SAF-2013-42920R and SAF2016-79040Rto D.S. D.S. also received 635122-PROCROP H2020 from the European Commission and ERC CoG 725091 from the European Research Council (ERC). ERC AdG 692511 PROVASC from the ERC and SFB1123-A1 from the Deutsche Forschungsgemeinschaft were given to C.W.; MHA VD1.2/81Z1600212 from the German Center for Cardiovascular Research (DZHK) was given to C.W. and O.S.; SFB1123-A6 was given to O.S.; SFB914-B08 was given to O.S. and C.W.; and INST 211/604-2, ZA 428/12-1, and ZA 428/13-1 were given to A.Z. This study was also supported by PI12/00494 from Fondo de Investigaciones Sanitarias (FIS) to C.M.; PI13/01979, Cardiovascular Network grant RD 12/0042/0054, and CIBERCV to B.I.; SAF2015-65607-R, SAF2013-49662-EXP, and PCIN-2014-103 from MEIC; and co-funding by Fondo Europeo de Desarrollo Regional (FEDER) to A.H. The CNIC is supported by the MEIC and the Pro CNIC Foundation and is a Severo Ochoa Center of Excellence (MEIC award SEV-2015-0505).S

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

Rational enzyme engineering of heme peroxidases through biophysical and biochemical modeling

[eng] Enzymes are proteins that catalyze biochemical reactions and their use report multiple advantages, as they can be very selective, low polluting (biodegradable), cheap and allow working in mild conditions compared with traditional non enzymatic processes. Despite their enormous benefits, their applications at the industrial level are still limited, mainly due to low productivity, low substrate tolerance (too specifics) and poor resistance to the industrial conditions, and for this reason, developing enhanced enzymes by means of enzyme engineering is a central research field nowadays. Notably, the application of computational chemistry in the field of enzyme engineering is increasing due to improvements in hardware and software. Moreover, this process is fast and low-priced and therefore, profitable for the application to the real problems that face industry. Therefore, motivated by this progress, the main goal of this thesis is the development of computational strategies that allow designing and evaluating modifications in enzymes, also aiming to obtain results quickly and inexpensively. This purpose was reached by the combination of different in silico methodologies that were further supported by experimental data in an interactive feedback process. As a result of this thesis, the enzymatic process in heme peroxidases was first satisfactorily described by dividing the process into two steps (from the ligand diffusion to the chemical reaction), using a combination of different computational techniques. The first step, which involves the protein/ligand recognition, was characterized with different molecular mechanics based techniques (MD, Docking and MC-PELE). On the other hand, the chemical reaction (including bond formation and electron transfer) was reproduced using QM based methods by means of energy calculation, spin density characterization, e-coupling calculations and QM/MM e-pathways descriptions. Following this procedure, the oxidation of veratryl alcohol by the enzyme lignin peroxidase was also characterized. Moreover, regarding the e-coupling calculations, a server to compute this vale faster and easy was developed. In the second part of the thesis, the results demonstrated that our protocol could reliably describe and predict enzymatic functions, not only in native enzymes but also in mutated ones, which results were in agreement with experimental data. For example, the structural implications over the reactivity in manganese peroxidase and its engineered variant obtained by cutting the last terminal residues were identified and characterized by the combination of Monte Carlo simulations (PELE) and electronic coupling calculations. The pH resistance in the mutant 2-1B (which was obtained experimentally by random directed evolution) in contrast with the wild type versatile peroxidase, were also rationalized by molecular dynamics, where the residues in the heme environment presented different conformation due to the mutations introduced, resulting in different pH resistance. Interestingly, the last part of the thesis was centered of engineering heme peroxidases. We engineered a peroxidase from in silico predictions to elucidate the long range electron transfer processes involved in the oxidation of the substrate veratryl alcohol by the enzyme versatile peroxidase. In this work we identify the key residues involved in the process, with further applications in engineering enhanced enzymes. Moreover, an enhanced manganese peroxidase mutant from a complete computational study was designed. First, the ligand diffusion study allowed finding the key aminoacids in the substrate/enzyme recognition and binding. Then, the chemical reaction in terms of the oxidation probability and kinetic constant for the proposed mutant were estimated, and the results were in agreement with experimental data. Therefore, the work of this thesis probed that computational biophysics and biochemistry are promising and valuable tools for enzyme engineering. In particular, in the field of rational design of heme peroxidases, they provide relevant information about the enzymatic mechanism and allow designing new enzymes, as well as checking their improvement/worsening, in an efficient way.[spa] Las enzimas son proteínas que catalizan reacciones bioquímicas y cuyo uso aporta múltiples ventajas, ya que son en general muy selectivas, poco contaminantes (biodegradables), baratas y permiten trabajar en condiciones suaves, en comparación con los procesos tradicionales no enzimáticos. A pesar de sus enormes beneficios, sus aplicaciones a nivel industrial son todavía limitadas, debido principalmente a la baja productividad, baja tolerancia al sustrato (demasiado específicos) y una escasa resistencia a las condiciones industriales en general, y por esta razón el desarrollo de enzimas mejoradas es un campo de investigación muy importante hoy en día. En particular, la aplicación de la química computacional en el campo de la ingeniería de enzimas está en aumento debido a las mejoras en hardware y software. Motivado por este progreso, el objetivo principal de esta tesis es el desarrollo de estrategias de cálculo que, mediante la combinación de diferentes metodologías in silico permitan diseñar y evaluar modificaciones en las enzimas, centrándonos en la obtención de resultados de forma rápida y económica. La primera parte de la tesis está centrada en la descripción del mecanismo enzimático entendido como un proceso de dos pasos que incluyen la difusión ligando y la reacción química, mediante una combinación de diferentes técnicas computacionales. El primer paso, que implica el reconocimiento de la proteína / ligando, se caracterizó con diferentes técnicas basadas en la mecánica molecular (dinámica molecular, docking y Monte Carlo- PELE). Por otro lado, la reacción química (incluyendo la formación de enlaces y la transferencia de electrones) se simuló usando métodos basados en mecánica cuántica por medio de cálculos de energía, la caracterización del spin o cálculos de acoplamiento electrónico. Por ejemplo, siguiendo este procedimiento, se caracterizó la oxidación de alcohol veratrílico por medio de la enzima lignin peroxidasa. Además, con el objetivo de poder calcular los acoplamientos electrónicos de una manera más rápida y fácil, se desarrolló un servidor web: ecoupling server. En la segunda parte de la tesis, los resultados demostraron que el protocolo anterior podría describir funciones enzimáticas no sólo en las especies nativas sino también en las variantes mutadas. Por ejemplo, se identificaron las implicaciones estructurales de la reactividad en una manganeso peroxidasa de la subfamilia larga y su variante modificada obtenida mediante la reducción de los últimos residuos terminales gracias al estudio de simulaciones de Monte Carlo (PELE) y cálculos de acoplamiento electrónico. Además, la resistencia a pH ácido en el mutante 2-1B (que se había obtenido previamente por evolución dirigida al azar) se comparó con la especie nativa y también se racionalizó por dinámica molecular, donde se observó que los residuos del entorno del hemo presentaban diferente conformación debido a las mutaciones introducidas, resultando en una diferente resistencia a pH ácido. La última parte de la tesis se centra en la ingeniería racional de hemo peroxidasas. A partir de predicciones in silico se diseñaron variantes de peroxidasa versátil para tratar de entender los procesos de transferencia electrónica de largo alcance que participan en la oxidación del sustrato de alcohol veratrílico, mediante la identificación de los residuos intermedios involucrados en el proceso. Además, a partir de un estudio computacional completo, se diseñó un mutante mejorado de manganeso peroxidasa, cuyos valores cinéticos estimados computacionalmente se encontraban de acuerdo con los resultados experimentales. En conclusión, en esta tesis se ilustra cómo los métodos biofísicos y bioquímicos computacionales son herramientas prometedoras y valiosas para la ingeniería de enzimas, en particular en el campo del diseño racional

Ecoupling server: A tool to compute and analyze electronic couplings

Electron transfer processes are often studied through the evaluation and analysis of the electronic coupling (EC). Since most standard QM codes do not provide readily such a measure, additional, and user-friendly tools to compute and analyze electronic coupling from external wave functions will be of high value. The first server to provide a friendly interface for evaluation and analysis of electronic couplings under two different approximations (FDC and GMH) is presented in this communication. Ecoupling server accepts inputs from common QM and QM/MM software and provides useful plots to understand and analyze the results easily. The web server has been implemented in CGI-python using Apache and it is accessible at http://ecouplingserver.bsc.es. Ecoupling server is free and open to all users without login.This work has been funded by the Spanish Ministry of Education and Science through the Project CTQ2013-48287.Peer Reviewe