Calcium regulates many biological processes through interaction with proteins with different conformational, dynamic, and metal binding properties. Previous studies have shown that the electrostatic environment plays a key role in calcium binding affinity. In this research, we aim to dissect the contribution of the electrostatic environment to calcium binding affinity using protein design. Many natural calcium binding proteins undergo large conformational changes upon calcium binding which hampers the study of these proteins. In addition, cooperativity between multiple calcium binding sites makes it difficult to study site-specific binding affinity. The design of a single calcium binding site into a host system eliminates the difficulties that occur in the study of calcium binding affinity. Using a computer algorithm we have rationally designed several calcium binding sites with a pentagonal bipyramidal geometry in the non-calcium dependent cell adhesion protein CD2 (CD2-D1) to better investigate the key factors that affect calcium binding affinity. The first generation proteins are all in varying electrostatic environments. The conformational and metal binding properties of each of these designed proteins were analyzed. The second generation designed protein, CD2.6D79, was designed based on criteria learned from the first generation proteins. This protein contains a novel calcium binding site with ligands all from the â-strands of the non-calcium dependent cell adhesion protein CD2. The resulting protein maintains native secondary and tertiary packing and folding properties. In addition to its selectivity for calcium over other mono and divalent metal ions, it displays strong metal binding affinities for calcium and its analogues terbium and lanthanum. Furthermore, our designed protein binds CD48, the ligand binding partner of CD2, with an affinity three-fold stronger than CD2. The electrostatic potential of the calcium binding site was modified through mutation to facilitate the study of the effect of electrostatic interactions on calcium binding affinity. Several charge distribution mutants display varying metal binding affinities based on their charge, distance to the calcium binding site, and protein stability. This study will provide insight into the key site factors that control calcium binding affinity and calcium dependent biological function.

Amyotrophic lateral sclerosis (ALS) is a debilitating, incurable, neurodegenerative disease characterized by degradation of motor neurons leading to paralysis and ultimately death in ~3-5 years. Approximately 10% of ALS cases have a dominant inheritance pattern, termed familial ALS (fALS). Mutations in the gene encoding the dimeric superoxide scavenger Cu, Zn superoxide dismutase (SOD), were found to be associated with ~20% of fALS cases. Over 110 predominantly missense SOD mutations lead to fALS by an unknown mechanism; however, it is thought that mutant SOD acquires a toxic gain of function. Mice as well as human post mortem studies have identified mutant SOD-rich aggregates in affected neurons, leading to the hypothesis that mutations in SOD increase the tendency of the protein to form toxic aggregates. SOD has a complex maturation process whereby the protein is synthesized in an apo or demetalated state, followed by formation of an intramolecular disulfide bond and binding of Zn2+ and Cu2+. Each of these post-translational modifications increases the stability of the protein. SOD has been shown to aggregate more readily from destabilized immature states, including the apo state both with and without the disulfide bond, highlighting the importance of these states. Thermal unfolding monitored by differential scanning calorimetry (DSC) and chemical denaturation monitored by optical spectroscopy were used to elucidate the folding mechanism and stability of both the apo SOD disulfide-intact and disulfide-reduced states. Chemically and structurally diverse fALS-associated mutants were investigated to gain insights into why mutant SODs may be more prone to misfold and ultimately aggregate. The mutations were introduced into a pseudo wild-type (PWT) background lacking free cysteines, resulting in highly reversible unfolding amenable to accurate thermodynamic analysis. Similarly to what was previously described for fully metallated (holo) SODs, chemical denaturation of the apo disulfide-intact SODs is well described by a 3-state dimer mechanism with native dimer, monomeric intermediate and unfolded monomer populated at equilibrium. Although removal of metals has a relatively small effect on the stability of the dimer interface, the stability of the monomer intermediate is dramatically reduced. Thermal unfolding of some disulfide-intact apo SOD mutants as well as PWT is well described by a 2-state dimer mechanism, while others unfold via a 3-state mechanism similar to chemical denaturation. All but one of the studied disulfide-intact apo mutations are destabilizing as evidenced by reductions in ΔG of unfolding. Additionally, several mutants show an increased tendency to aggregate in thermal unfolding studies through increased ratios of van’t Hoff to calorimetric enthalpy (HvH/ Hcal ). The effects of the mutations on dimer interface stability in the apo disulfide-intact form were further investigated by isothermal titration calorimetry (ITC) which provided a quantitative measure of the dissociation constant of the dimer (Kd). ITC results revealed that disulfide-intact apo SOD mutants generally have increased Kd values and hence favor dimer dissociation to the less stable monomer which has been proposed to be a precursor to toxic aggregate formation. Reduction of the disulfide bond in apo SOD leads to marked destabilization of the dimer interface, and both thermal unfolding and chemical denaturation of PWT and mutants are well described by a 2-state monomer unfolding mechanism. Most mutations destabilize the disulfide-reduced apo SOD to such an extent that the population of unfolded monomer under physiological conditions exceeds 50%. The disulfide-reduced apo mutants show increased tendency to aggregate relative to PWT in DSC experiments through increased HvH /Hcal, low or negative change in heat capacity of unfolding and/or decreased unfolding reversibility. Further evidence of enhanced aggregation tendency of disulfide-reduced apo mutants was derived from analytical ultracentrifugation sedimentation equilibrium experiments that revealed the presence of weakly associated aggregates. Overall, the results presented here provide novel insights into SOD maturation and the possible impact of stability on aggregation.

Amyotrophic lateral sclerosis (ALS) is a debilitating, incurable, neurodegenerative disease characterized by degradation of motor neurons leading to paralysis and ultimately death in ~3-5 years. Approximately 10% of ALS cases have a dominant inheritance pattern, termed familial ALS (fALS). Mutations in the gene encoding the dimeric superoxide scavenger Cu, Zn superoxide dismutase (SOD), were found to be associated with ~20% of fALS cases. Over 110 predominantly missense SOD mutations lead to fALS by an unknown mechanism; however, it is thought that mutant SOD acquires a toxic gain of function. Mice as well as human post mortem studies have identified mutant SOD-rich aggregates in affected neurons, leading to the hypothesis that mutations in SOD increase the tendency of the protein to form toxic aggregates. SOD has a complex maturation process whereby the protein is synthesized in an apo or demetalated state, followed by formation of an intramolecular disulfide bond and binding of Zn2+ and Cu2+. Each of these post-translational modifications increases the stability of the protein. SOD has been shown to aggregate more readily from destabilized immature states, including the apo state both with and without the disulfide bond, highlighting the importance of these states. Thermal unfolding monitored by differential scanning calorimetry (DSC) and chemical denaturation monitored by optical spectroscopy were used to elucidate the folding mechanism and stability of both the apo SOD disulfide-intact and disulfide-reduced states. Chemically and structurally diverse fALS-associated mutants were investigated to gain insights into why mutant SODs may be more prone to misfold and ultimately aggregate. The mutations were introduced into a pseudo wild-type (PWT) background lacking free cysteines, resulting in highly reversible unfolding amenable to accurate thermodynamic analysis. Similarly to what was previously described for fully metallated (holo) SODs, chemical denaturation of the apo disulfide-intact SODs is well described by a 3-state dimer mechanism with native dimer, monomeric intermediate and unfolded monomer populated at equilibrium. Although removal of metals has a relatively small effect on the stability of the dimer interface, the stability of the monomer intermediate is dramatically reduced. Thermal unfolding of some disulfide-intact apo SOD mutants as well as PWT is well described by a 2-state dimer mechanism, while others unfold via a 3-state mechanism similar to chemical denaturation. All but one of the studied disulfide-intact apo mutations are destabilizing as evidenced by reductions in ΔG of unfolding. Additionally, several mutants show an increased tendency to aggregate in thermal unfolding studies through increased ratios of van’t Hoff to calorimetric enthalpy (HvH/ Hcal ). The effects of the mutations on dimer interface stability in the apo disulfide-intact form were further investigated by isothermal titration calorimetry (ITC) which provided a quantitative measure of the dissociation constant of the dimer (Kd). ITC results revealed that disulfide-intact apo SOD mutants generally have increased Kd values and hence favor dimer dissociation to the less stable monomer which has been proposed to be a precursor to toxic aggregate formation. Reduction of the disulfide bond in apo SOD leads to marked destabilization of the dimer interface, and both thermal unfolding and chemical denaturation of PWT and mutants are well described by a 2-state monomer unfolding mechanism. Most mutations destabilize the disulfide-reduced apo SOD to such an extent that the population of unfolded monomer under physiological conditions exceeds 50%. The disulfide-reduced apo mutants show increased tendency to aggregate relative to PWT in DSC experiments through increased HvH /Hcal, low or negative change in heat capacity of unfolding and/or decreased unfolding reversibility. Further evidence of enhanced aggregation tendency of disulfide-reduced apo mutants was derived from analytical ultracentrifugation sedimentation equilibrium experiments that revealed the presence of weakly associated aggregates. Overall, the results presented here provide novel insights into SOD maturation and the possible impact of stability on aggregation.

The primary objective was to study the kinetics of folding of RNase Sa. Wild-type RNase Sa does not contain tryptophan. A tryptophan was substituted at residue 81 (WT*) to allow fluorescence spectroscopy to be used to monitor folding. This tryptophan mutation did not change the stability. An analysis of the folding kinetics of RNase Sa showed two folding phases, indicating the presence of an intermediate and consistent with the following mechanism: D ↔ I ↔ N. Both refolding limbs of the chevron plot (abcissa = final conc. of denaturant and ordinate = kinetic rate) had non-zero slopes suggesting that proline isomerization was not rate-limiting. The conformational stability of a charge-reversed variant, WT*(D17R), of a surface exposed residue on RNase Sa has been studied by equilibrium techniques. This mutant with a single amino acid charge reversal of a surface exposed residue resulted in decreased stability. Calculations using Coulomb’s Law suggested that favorable electrostatic interactions in the denatured state were the cause for the decreased stability for the charge-reversed variant. Folding and unfolding kinetic studies were designed and conducted to study the charge-reversal effect. Unfolding kinetics showed a 10-fold increase in the unfolding rate constant for WT*(D17R) over WT* and no difference in the rate of refolding. Kinetics experiments were also conducted at pH 3 where protonation of Asp17 (charge reversal site) would be expected to negate the observed kinetic effect. At pH 3 the kinetics of unfolding of WT* RNase Sa and the WT*(D17R) mutant were more similar. These kinetic results indicate that a single-site charge reversal lowered the free energy of the denatured state as suspected. Additionally, the results showed that the transition state was stabilized as well. These results show that a specific Coulombic interaction lowered the free energy in the denatured and transition state of the charge-reversal mutant, more than in WT*. To our knowledge, this is the first demonstration that a favorable electrostatic interaction in the denatured state ensemble has been shown to influence the unfolding kinetics of a protein.

Recent advances in molecular biology have led to an explosive growth in the number of peptide and protein drugs derived from both recombinant technology and conventional peptide drug design. However, development of peptide and protein therapeutics has proven to be very challenging because of inadequate physical and chemical stability. In recent years, particle engineering processes have become promising approaches for enhancement of protein stability as well as provide options for more delivery routes. In this research program, spray freezing into liquid (SFL) process was developed and optimized in order to achieve broad platform and application in protein and peptide drug delivery systems. The overall goal of this research was to produce stabilized protein and peptide microparticles for various drug delivery systems by using SFL particle engineering technology. Firstly, the use of the SFL process to produce peptide microparticles was investigated. Insulin microparticles produced by the SFL process were highly porous, low tap density and narrow particle size distribution. The influence of the SFL process parameters and excipients on the physicochemical properties of peptide microparticles was determined and compared to the widely used particle formation technique--freeze-drying. The SFL process was further used to produce protein microparticles. In the study, bovine serum albumin (BSA), a medium sized protein, was used as a model drug. The influence of SFL process parameters and excipients on the stability of BSA was studied. Very low monomer loss of BSA was found in this study even though the specific surface area of the powder was very high. Results also demonstrated that the SFL process had minimal influence on protein structure. The SFL process was further investigated by comparing the SFL process to spray freeze drying process (SFD), which is a relatively new process to produce protein and peptide microparticles. The influence of atomization, freezing and drying on the stability of lysozyme was investigated for both the SFL and SFD process. This study tested the hypothesis that the SFL process is a better process than SFD process because of avoiding air-liquid interface and minimum interfacial surface absorption of protein in SFL process. The particle size of protein and peptide microparticles produced by SFL process was further reduced to nanoparticles by sonication or homogenization processes in organic solvent. In this study, the influence of process parameters on the particle size and enzyme activity of lysozyme was investigated. The results showed that sonication or homogenization did not influence the enzyme activity of lysozyme. Lastly, insulin and insulin/dextran microparticles produced by SFL the process was encapsulated into polymer microspheres for oral delivery. Complexation and polymer composition was studied in order to optimize release and stability of insulin. Insulin nanoparticles in microspheres minimized the release of insulin in acid with high drug loading compared to other studies. The stability of insulin was decreased by complexation to dextran sulfate. The results of this research demonstrated that the SFL process offers a highly effective approach to produce protein and peptide powders suitable for different drug delivery systems. The microparticles produced by the SFL process had desirable characteristics such as narrow particle size distribution and high porosity. The stability of protein and peptide was well maintained through the SFL process. Therefore, SFL process is an effective particle engineering process for protein and peptide pharmaceuticals. / text

The World Health Organization has identified antimicrobial resistance as one of the top three threats to human health. Gram-negative bacteria such as Escherichia coli are intrinsically more resistant to antimicrobials. There are very few drugs either on the market or in the pharmaceutical pipeline targeting Gram-negative pathogens. Two mechanisms, the protection of the outer membrane and the active efflux by the multidrug transporters, play important roles in conferring multidrug resistance to Gram-negative bacteria. My work focuses on two main directions, each aligning with one of the known multidrug resistance mechanisms. The first direction of my research is in the area of the biogenesis of the bacterial outer membrane. The outer membrane serves as a permeability barrier in Gram-negative bacteria. Antibiotics cross the membrane barrier mainly via diffusion into the lipid bilayer or channels formed by outer membrane proteins. Therefore, bacterial drug resistance is closely correlated with the integrity of the outer membrane, which depends on the correct folding of the outer membrane proteins. The folding of the outer membrane proteins has been studied extensively in dilute buffer solution. However, the cell periplasm, where the folding actually occurs, is a crowded environment. In Chapter 2, effects of the macromolecular crowding on the folding mechanisms of two bacterial outer membrane proteins (OmpA and OmpT) were examined. Our results suggested that the periplasmic domain of OmpA improved the efficiency of the OmpA maturation under the crowding condition, while refolding of OmpT was barely affected by the crowding. The second direction of my research focuses on the major multidrug efflux transporter in Gram-negative bacteria, AcrB. AcrB is an obligate trimer, which exists and functions exclusively in a trimeric state. In Chapter 3, the unfolding of the AcrB trimer was investigated. Our results revealed that sodium dodecyl sulfate induced unfolding of the trimeric AcrB started with a local structural rearrangement. While the refolding of secondary structure in individual monomers could be achieved, the re-association of the trimer might be the limiting factor to obtain folded wild type AcrB. In Chapter 4, the correlation between the AcrB trimer stability and the transporter activity was studied. A non-linear correlation was observed, in which the threshold trimer stability was required to maintain the efflux activity. Finally, in Chapter 5, the stability of another inner membrane protein, AqpZ, was studied. AqpZ was remarkably stable. Several molecular engineering approaches were tested to improve the thermal stability of the protein.

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease causing degeneration of upper and lower motor neurons. Most ALS cases are sporadic; only 6% are associated with mutations in Cu, Zn superoxide dismutase (SOD1). It is believed, however, that sporadic and familiar forms of ALS share a common mechanism, where SOD1 plays an important role: SOD1 knockout mice do not develop ALS, whereas the overexpression of human SOD1 in mice produces ALS-like symptoms. Increasing evidence suggest that the SOD1 structure gains cytotoxic properties, but detailed description of the toxic species is missing. This thesis work is focused on understanding how structural and dynamic properties of SOD1 change along its folding free-energy landscape and indicates the structural hot-spots from where the cytotoxic species may originate. Thus, binding of the zinc controls folding, stability and turnover of SOD1: (i) miscoordination of Zn2+ by the Cu-ligands speeds up folding of the SOD1 core structure, however, it stabilizes SOD1 in a state where both active-site loops IV and VII are unfolded, (ii) coordination of Zn2+ in the Zn-site, induces the folding of loop VII and stabilizes the native and  functional fold of both active-site loops and (iii) the tremendous stability gain due to Zn-site metallation corresponds to a folded state’s lifetime of  &gt; 100 years, thus the cellular lifetime of SOD1 is likely controlled by Zn2+ release, which again is coupled to opening of active-site loops. Hence the active-site loops IV and VII stand out as critical and floppy parts of the SOD1 structure. Moreover, a number of ALS-associated mutations, benign to apo-SOD1 stability, are shown here to affect integrity of active-site loops in holo-SOD1, which, in turn, increases population of SOD1 species with these loops disorganized. Finally, the close relation between SOD1 and Zn2+ can also act in the reverse direction: a perturbed folding free-energy landscape of SOD1 can disturb Zn2+ homeostasis. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 4: Manuscript.</p>

The work in this thesis focuses on the study of three main aspects of proteins, viz, Protein structure, stability, and dynamics. Chapter 1 is a general introduction to the topics studied in this thesis. Chapter 2 deals with the first aspect, i.e., protein structure in which we describe an approach to use saturation mutagenesis phenotypes to guide protein structure prediction. Chapters 3 and 4 discuss how to increase protein stability using surface electrostatics, and Chapter 5 details a method to predict whether a proline substitution in a given protein would be stabilizing or destabilizing. Hence, Chapters 3-5 can be associated with the second aspect, i.e., protein stability. The third aspect, namely protein dynamics, is dealt with in Chapters 6 and 7 which study conformational dynamics of adenylate kinase. Protein structure prediction is a difficult problem with two major bottlenecks, namely, generation of accurate models and the selection of the most appropriate models from a large pool of decoys. In Chapter 2, the problem of model discrimination is addressed using mutant phenotype information derived from saturation mutagenesis library. A library of ~1500 single-site mutants of the E. coli toxin CcdB (Controller of Cell Division or Death B) has been previously constructed in our lab. The pooled library was characterized in terms of individual mutant phenotypes at various expression levels which were derived from the relative populations of mutants at each expression level. The relative populations of mutants were estimated using deep sequencing. Mutational tolerances were derived from the phenotypic data and were used to define an empirical parameter which correlated with a structural parameter, residue depth. We further studied how this new parameter can be used for model discrimination. Increasing protein stability in a rational way is a challenging problem and has been addressed by various approaches. One of the most commonly used approaches is optimization of protein core residues. Recently, optimization of protein surface electrostatics has been shown to be a useful approach for increasing stability of proteins. In Chapter 3, from analyses of a dataset of ~1750 non-homologues proteins, we show that proteins having a pI away from physiological pH, possess a significant fraction of unfavorably placed charged amino acids on their surface. One way to increase protein stability in such cases might be to alter these surface charges. This hypothesis was validated experimentally by making charge reversal mutations at putative unfavorable positions on the surface of maltose binding protein, MBP. The observed stabilization can potentially be increased by combining multiple individually stabilizing mutations. Different combinations of such mutations were made and tested in Chapter 4 to decide which mutants can be combined to achieve net stabilization. Ideas were tested through systematic experimentation which involved generation of two-site, three-site, and four-site mutations. A maximum increase in melting temperature (Tm) of 3-4 °C over wild-type protein was achieved upon combination of individually stabilizing mutants. Proline (Pro) has two special stereo-chemical properties when it is a part of a polypeptide chain. First the φ value of Pro has a very constrained distribution and second, Pro lacks an amide hydrogen. Due to these properties, introduction of Pro might perturb stability/activity of the protein. In Chapter 5 we describe a procedure to accurately predict the effects of Pro introduction on protein stability. Pro scanning mutagenesis was carried out on the model protein CcdB and the in vivo activity of the individual mutants was also examined. A decision tree was constructed, using the special stereo-chemical properties of Pro to maximize correlation of predicted phenotype with the in vivo activity. Binary classification as perturbing or non-perturbing of every Pro substitution was possible using the decision tree. The performance of the decision tree was assessed on various test systems, and the average accuracy was found to be ~75%. The role of conformational dynamics in enzyme catalysis has been explored in great detail in the literature. In Chapter 6, with the help of very long (350 ns), fully atomistic, explicit solvent molecular dynamics simulations, we studied conformational dynamics of adenylate kinase. We found the existence of a relatively stable state which lies intermediate between the open and closed conformations of the enzyme. The finding was further confirmed by computing a two dimensional configurational free energy surface when motions along each of the two movable domains (LID and NMP) are considered as reaction coordinates. We also discussed possible roles of the intermediate state during enzyme catalysis. The role of water in stabilization of intermediate states was also discussed. In Chapter 7, we studied dynamical coupling between LID and NMP domains of adenylate kinase during domain opening. Our observation suggests that the LID domain should start opening prior to the NMP domain. On the domain opening trajectory, the free energy surface of LID domain was found to be very rugged. We discuss a possible role of water in the ruggedness of the domain motions. The Appendix contains 3 supplementary parts of the thesis. Appendix I is a mutant dataset obtained from 454 sequencing analysis. It includes the normalized number of reads per mutation at each expression level along with mutational sensitivity score. Appendix II is parameters used for one of the electrostatic calculations. Appendix III contains a list of PDB ids used for database analysis in surface electrostatics work discussed in Chapter 3.

Traditional computational protein design (CPD) calculations model sequence perturbations and evaluate their stabilities using a single fixed protein backbone template in an approach referred to as single‐state design (SSD). However, certain design objectives require the explicit consideration of multiple conformational states. Cases where a multistate framework may be advantageous over the single‐state approach include the computer aided discovery of new enzyme substrates, the prediction of protein stabilities, and the design of protein dynamics. These design objectives can be tackled using multistate design (MSD). However, it is often the case that a design objective requires the consideration of a protein state having no available structure information. For such circumstances the multistate framework cannot be applied. In this thesis I present the development of two template and ensemble preparation methodologies and their application to three projects. The purpose of which is to demonstrate the necessary ensemble modeling strategies to overcome limitations in available structure information. Particular emphasis is placed on the ability to recapitulate experimental data to guide modelling of the design space. Specifically, the use of MSD allowed for the accurate prediction of a methyltransferase recognition motif and new substrates, the prediction of mutant sequence stabilities with quantitative accuracy, and the design of dynamics into the rigid Gβ1 scaffold producing a set of dynamic variants whose tryptophan residue exchanges between two conformations on the millisecond timescale. Implementation of both the ensemble, coordinate perturbation followed by energy minimization (PertMin), and template, rotamer optimization followed by energy minimization (ROM), generation protocols developed here allow for exploration and manipulation of the structure space enabling the success of these applications.

Cieľom tejto práce je vytvorenie novej databázy dát pre proteínovú stabilitu, ktorá bude udržiavať a poskytovať experimentálne dáta. Výsledkom práce je databáza FireProtDB, ktorá poskytuje manuálne overené experimentálne dáta z dostupných zdrojov a implementuje grafické užívateľské rozhranie, ktoré poskytuje dôležité informácie o dátach spoločne s možnosťou vyhľadávania umožňujúcim vytvárať dotazy na mieru a cieliacim na užívateľov, ktorí hľadajú dáta pre vytváranie dátových sád pre nástroje využívajúce strojové učenie.