Yes / A reliable description of ion pair interactions for biological systems, particularly those involving polyatomic ions such as carboxylate and divalent ions such as Ca2+, using biomolecular force-fields is essential for making useful predictions for a range of protein functions. In particular, the interaction of divalent ions with the double carboxylate group present in γ-carboxyglutamic acid (Gla), relevant to the function of many proteins, is relatively understudied using biomolecular force-fields. Using force-field based metadynamics simulations to predict the free energy of binding between Ca2+ and the carboxylate group in liquid water, we show that a widely-used biomolecular force-field, CHARMM22*, substantially over-estimates the binding strength between Ca2+ and the side-chains of both glutamic acid (Glu) and Gla, compared with experimental data obtained for the analogous systems of aqueous calcium–acetate and calcium–malonate. To correct for this, we propose and test a range of modifications to the σ value of the heteroatomic Lennard–Jones interaction between Ca2+ and the oxygen of the carboxylate group. Our revised parameter set can recover the same three association modes of this aqueous ion pair as the standard parameter set, and yields free energies of binding for the carboxylate–Ca2+ interaction in good agreement with experimental data. The revised parameter set recovers other structural properties of the ion pair in agreement with the standard CHARMM22* parameter set.

The complexity of all biomolecules in existence today can be attributed to the variation of the amino acid repertoire. In nature, 20 canonical amino acids are translated to form these biomolecules, however, many of these amino acids have revealed posttranslational modifications (i.e. acetylation, methylation) after incorporation. Amino acids that exhibit PTM are known for their involvement in cellular processes such as DNA repair and DNA replication; these PTMs are commonly found on histones within the chromatin complex. Utilization of in vivo site-specific incorporation has recently reported functionality of post-translationally modified amino acids.1 xii Here we report the synthesis and in vivo site-specific incorporation of the histone PTM, 2-hydroxyisobutyrl lysine (Khib), with the pyrrolysyl tRNA/ RNA synthetase system. This translational machine can better serve to probe Khib for functional benefits. Additionally, this thesis focuses much of its attention on the development of unnatural amino acids (UAA) with optogenetic characteristics. These UAAs, if site-specifically incorporated, can be used to control enzymes and proteins through rapid light perturbation (365nm UV light). Furthermore, discussed is the synthesis of photo-caged threonine and photo-caged serine as potential substrates for the pyrrolysyl translational machinery.

Production of mutant biological molecules for understanding biological principles or as therapeutic agents has gained considerable interest recently. Synthetic genes are today being widely used for production of such molecules due to the substantial decrease in the costs associated with gene synthesis technology. Along one such line, we have engineered tRNA genes in order to dissect the effects of G:U base-pairs on the accuracy of the protein translation machinery. Our results provide greater detail into the thermodynamic interactions between tRNA molecules and an Elongation Factor protein (termed EF-Tu in bacteria and eEF1A in eukaryotes) and how these interactions influence the delivery of aminoacylated tRNAs to the ribosome. We anticipate that our studies not only shed light on the basic mechanisms of molecular machines but may also help us to develop therapeutic or novel proteins that contain unnatural amino acids. Further, the manipulation of the translation machinery holds promise for the development of new methods to understand the origins of life. Along another line, we have used the power of synthetic biology to experimentally validate an evolutionary model. We exploited the functional diversity contained within the EF-Tu/eEF1A gene family to experimentally validate the model of evolution termed ‘heterotachy’. Heterotachy refers to a switch in a site’s mutational rate class. For instance, a site in a protein sequence may be invariant across all bacterial homologs while that same site may be highly variable across eukaryotic homologs. Such patterns imply that the selective constraints acting on this site differs between bacteria and eukaryotes. Despite intense efforts and large interest in understanding these patterns, no studies have experimentally validated these concepts until now. In the present study, we analyzed EF-Tu/eEF1A gene family members between bacteria and eukaryotes to identify heterotachous patterns (also called Type-I functional divergence). We applied statistical tests to identify sites possibly responsible for biomolecular functional divergence between EF-Tu and eEF1A. We then synthesized protein variants in the laboratory to validate our computational predictions. The results demonstrate for the first time that the identification of heterotachous sites can be specifically implicated in functional divergence among homologous proteins. In total, this work supports an evolutionary synthetic biology paradigm that in one direction uses synthetic molecules to better understand the mechanisms and constraints governing biomolecular behavior while in another direction uses principles of molecular sequence evolution to generate novel biomolecules that have utility for industry and/or biomedicine.

Bio-nanohybrid materials based on the combination of biomolecules and inorganic supports are interesting by their versatile applications in regenerative medicine, drug delivery, bio-engineering and catalysis. In that context, understanding of organic/inorganic interactions offers an important key to design new and more complex bio-systems with modified interactions. In this thesis, amino acids and synthesised poly-amino acids were immobilised in hydrotalcite-like materials under green, controllable and efficient protocols. Additionally, these nanohybrid materials were used as heterogenized catalysts exhibiting high catalytic activity and selectivity in comparison with their counterpart components. All result data showed that the location and nature of the immobilization had an important role in the final chemical properties; moreover, this novel bio-nanohybrid material exhibited excellent synergistic behaviour which was unique for each material and could be modified according with the reaction requirements. All novel bio-nanohybrid materials were easily synthesised, recovered and, in some cases, reused without appreciable deactivation. / Materiales bio-nanohíbridos compuestos por la combinación de biomoléculas y soportes inorgánicos son interesantes por sus versátiles aplicaciones en medicina regenerativa, transporte de medicamentos, bio-ingeniería y catálisis. En este contexto, el entendimiento de las interacciones orgánico/inorgánicas ofrece importante información para el diseño de nuevos y más complejos bio-sistemas con interacciones modificadas. En esta tesis, amino ácidos y poli-amino ácidos sintéticos fueron inmovilizados en materiales tipo hidrotalcita a través de eficientes y controlables protocolos amigables con el medioambiente. Adicionalmente, estos materiales fueron usados como catalizadores heterogeneizados mostrando alta actividad y selectividad en comparación con sus componentes de partida. En este sentido, la localización y naturaleza de la interacción tuvo un importante rol en las propiedades catalíticas finales; además, estos novedosos materiales mostraron un excelente comportamiento sinérgico el cual fue único y pudo ser modificado de acuerdo a las necesidades en reacción. Todos los materiales bio-nanohíbirdos fueron sintetizados y recuperados con facilidad del medio de reacción y en algunos casos fueron reutilizados sin desactivación apreciable.

Thesis (doctoral)--Universitetet i Lund. / Reprints of journal articles inserted in pocket inside back cover.

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Fourteen Ball State University softball players participated in this study to examine the effects of an amino acid supplement, Rebuild II TM, on strength and performance. Rebuild II TM contains high levels of BCAAs and glutamine. Two groups strength trained for ten weeks with the treatment group consuming Rebuild II TM, and the control group consuming a placebo. Subjects were pre and post-tested on the bench press, squat and machine shoulder press for strength, and performed a 90-foot sprint and a vertical jump for performance measures. LBW was calculated from the subjects body weight and percent fat. Pre and post measures were analyzed using a two way Anova variance with repeated measures test with a significant level set at p< 0.05. Both groups showed significant increases in strength and vertical jump performance, but only the Rebuild II TM group had a significant increase in LBW and decrease in percent fat. It was concluded that with a controlled weight training program, softball players will increase strength and vertical jump performance, and by adding an amino acid supplement to an athletes diet, there may be larger increases in LBW and decreases in percent fat while strength training. / School of Physical Education

Thirteen Ball State University, male basketball players participated in this study to examine the effects of an amino acid supplement, Rebuild IITM and glutamine, on strength and vertical jump performance. Rebuild IITM contains high levels of BCAA and glutamine.The thirteen subjects were divided into two groups, Rebuild IIT"'' (n=7) and placebo (n=6). Both groups participated in a ten week strength and conditioning training program. Subjects were pre and post-tested on the hang clean, bench press, squat, and the vertical jump. Changes in percent body fat were also compared. Pre and post measures were analyzed using a 2x2 ANOVA variance with a significant level set at p<0.05. Both groups showed significant increases between pre and post-test measurements in all of the variables measured, but could not be significantly proven to be due to treatment effect. It was concluded that with a controlled strength and conditioning program, basketball players would increase strength and vertical jump performance and decrease percent body fat. Yet in order to determine whether an amino acid supplement may further increase these measurements, a dietary recall must be obtained. / School of Physical Education

Computer-mediated communication [CMC] is beginning to be used more frequently in traditional classrooms. A group of physical chemistry professors have developed Physical Chemistry On-Line [PCOL] modules designed to augment in-class instruction and engage students at geographically dispersed institutions in activities to help them learn physical chemistry concepts. These modules use context-rich scenarios with a guided-inquiry approach, and the WWW and e-mail for information distribution and communication. This allows for intra- and inter-institutional collaboration between module participants. Three modules implemented during the Fall 2000 term are evaluated in this study. In order to assess the effectiveness of PCOL, each student completed a pre-module and post-module survey, pre-module and post-module content questions, and participated in an online discussion group. The primary focus of this analysis was to determine the student's: 1) perception of on-line activities, 2) perception of on-line interactions, and 3) use of computers. / School of Physical Education

Thesis (doctoral)--Universitetet i Lund. / Reprints of journal articles inserted in pocket inside back cover.