Extending the Reach of Computational Approaches to Model Enzyme Catalysis

Recent years have seen tremendous developments in methods for computational modeling of (bio-) molecular systems. Ever larger reactive systems are being studied with high accuracy approaches, and high-level QM/MM calculations are being routinely performed. However, applying high-accuracy methods to large biological systems is computationally expensive and becomes problematic when conformational sampling is needed. To address this challenge, classical force field based approaches such as free energy perturbation (FEP) and empirical valence bond calculations (EVB) have been employed in this work. Specifically: Force-field independent metal parameters have been developed for a range of alkaline earth and transition metal ions, which successfully reproduce experimental solvation free energies, metal-oxygen distances, and coordination numbers. These are valuable for the computational study of biological systems. Experimental studies have shown that the epoxide hydrolase from Solanum tuberosum (StEH1) is not only an enantioselective enzyme, but for smaller substrates, displays enantioconvergent behavior. For StEH1, two detailed studies, involving combined experimental and computational efforts have been performed: We first used trans-stilbene oxide to establish the basic reaction mechanism of this enzyme. Importantly, a highly conserved and earlier ignored histidine was identified to be important for catalysis. Following from this, EVB and experiment have been used to investigate the enantioconvergence of the StEH1-catalyzed hydrolysis of styrene oxide. This combined approach involved wildtype StEH1 and an engineered enzyme variant, and established a molecular understanding of enantioconvergent behavior of StEH1. A novel framework was developed for the Computer-Aided Directed Evolution of Enzymes (CADEE), in order to be able to quickly prepare, simulate, and analyze hundreds of enzyme variants. CADEE’s easy applicability is demonstrated in the form of an educational example. In conclusion, classical approaches are a computationally economical means to achieve extensive conformational sampling. Using the EVB approach has enabled me to obtain a molecular understanding of complex enzymatic systems. I have also increased the reach of the EVB approach, through the implementation of CADEE, which enables efficient and highly parallel in silico testing of hundreds-to-thousands of individual enzyme variants

Comparing higher education preferences of students in EU and India: a cost Quality analysis

Šajā globalizācijas laikmetā vispasaules augstākās izglītības sistēma ir piedzīvojusi nemainīgas pārmaiņas, tautsaimniecība ir atvērta ne tikai tirdzniecības priekšrocībām, bet arī izglītības nozarēs ir notikusi lielāka liberalizācija. Eiropā un Indijā pasaulē ir vecākās izglītības sistēmas, un pašreizējā scenārijā tās pārvērtē augstāko izglītību attiecībā uz izmaksām, kvalitāti un piekļuvi. Izglītība šīm abām valstīm ir bijusi viena no galvenajām prioritātēm, un valsts augstskolas ir pazīstamas ar kvalitāti un izmaksu garantiju, ar nelielām atšķirībām starp tām, tāpēc tiek mēģināts veikt salīdzinošu pētījumu. Bet ir daži faktori, kas ietekmē indivīda lēmumu pieņemšanu, izvēloties viņu vēlamās institūcijas abās valstīs. Šī pētījuma mērķis ir sniegt priekšstatu par augstākās izglītības iestādēm un izglītības sektoru Deli, Indijā un Rīgā, kā arī analizēt saikni starp izmaksām un izglītības kvalitāti un to, cik lielā mērā šie faktori ietekmē lēmumu pieņemšanas izvēli no indivīda.. In this era of globalisation, worldwide higher education system has seen constant changes, economies have not only opened for trade benefits but much liberalization has been done in education sectors. Europe and India have the oldest education systems in the world and in the current scenario they are redefining the higher education with respect to cost, quality and access. Education has been one of the top priority for these two countries and public higher education institutions are known for their quality and cost assurance with little variations among them therefore, on these grounds a comparative study is attempted. But there are certain factors which affects the decision making of an individual in selecting their preferred institutions in the two countries. The purpose of this study is to provide a picture of the Higher Education Institutions and the education sector in Delhi, India and Riga, Latvia, also to analyse the relation between cost and quality of education and how far these factors affects the decision-making choice of an individual

Modeling catalytic promiscuity in the alkaline phosphatase superfamily

In recent years, it has become increasingly clear that promiscuity plays a key role in the evolution of new enzyme function. This finding has helped to elucidate fundamental aspects of molecular evolution. While there has been extensive experimental work on enzyme promiscuity, computational modeling of the chemical details of such promiscuity has traditionally fallen behind the advances in experimental studies, not least due to the nearly prohibitive computational cost involved in examining multiple substrates with multiple potential mechanisms and binding modes in atomic detail with a reasonable degree of accuracy. However, recent advances in both computational methodologies and power have allowed us to reach a stage in the field where we can start to overcome this problem, and molecular simulations can now provide accurate and efficient descriptions of complex biological systems with substantially less computational cost. This has led to significant advances in our understanding of enzyme function and evolution in a broader sense. Here, we will discuss currently available computational approaches that can allow us to probe the underlying molecular basis for enzyme specificity and selectivity, discussing the inherent strengths and weaknesses of each approach. As a case study, we will discuss recent computational work on different members of the alkaline phosphatase superfamily (AP) using a range of different approaches, showing the complementary insights they have provided. We have selected this particular superfamily, as it poses a number of significant challenges for theory, ranging from the complexity of the actual reaction mechanisms involved to the reliable modeling of the catalytic metal centers, as well as the very large system sizes. We will demonstrate that, through current advances in methodologies, computational tools can provide significant insight into the molecular basis for catalytic promiscuity, and, therefore, in turn, the mechanisms of protein functional evolution

CADEE: Computer-Aided Directed Evolution of Enzymes

The tremendous interest in enzymes as biocatalysts has led to extensive work in enzyme engineering, as well as associated methodology development. Here, a new framework for computer-aided directed evolution of enzymes (CADEE) is presented which allows a drastic reduction in the time necessary to prepare and analyze in silico semi-automated directed evolution of enzymes. A pedagogical example of the application of CADEE to a real biological system is also presented in order to illustrate the CADEE workflow

Force Field Independent Metal Parameters Using a Nonbonded Dummy Model

The cationic dummy atom approach provides a powerful nonbonded description for a range of alkaline-earth and transition-metal centers, capturing both structural and electrostatic effects. In this work we refine existing literature parameters for octahedrally coordinated Mn2+, Zn2+, Mg2+, and Ca2+, as well as providing new parameters for Ni2+, Co2+, and Fe2+. In all the cases, we are able to reproduce both M2+-O distances and experimental solvation free energies, which has not been achieved to date for transition metals using any other model. The parameters have also been tested using two different water models and show consistent performance. Therefore, our parameters are easily transferable to any force field that describes nonbonded interactions using Coulomb and Lennard-Jones potentials. Finally, we demonstrate the stability of our parameters in both the human and Escherichia coli variants of the enzyme glyoxalase 1 as showcase systems, as both enzymes are active with a range of transition metals. The parameters presented in this work provide a valuable resource for the molecular simulation community, as they extend the range of metal ions that can be studied using classical approaches, while also providing a starting point for subsequent parametrization of new metal centers