Akt activation mediates increases in glycogen synthesis in response to insulin in humans, while extracellular signal-regulated kinase (ERK) activation increases gene transcription and protein translation in response to endurance and resistance exercise. Akt activation increases only in response to intense muscle contractions and during hypertrophy in rats. No study has examined Akt and ERK activation with increasing numbers of intense muscle contractions in humans. Therefore, the primary objectives of this investigation were to determine if Akt activation increases in response to resistance exercise in humans, and to compare the changes in Akt and ERK activation in response to increasing numbers of muscle contractions.Akt and ERK activation were compared in muscle biopsy samples from 7 men before (Pre) and after (Post) knee extension and control protocols using enzyme linkedimmunosorbent assays. Baseline information was obtained including body composition and maximal strength (1-RM). Subjects were familiarized with knee extensions performed at 70% of 1-RM and a specified repetition cadence (2sec up, 2sec down). Once/wk, subjects performed one protocol in random order: 1 repetition (rep), 10reps, 3 sets of l0reps (3x10), or 6min of sitting. Akt activation decreased 42%, while ERK activation increased 108% in response to 3x10 (p<0.05). Akt and ERK activation did not change with 1 and 10reps, and thus their responses were not dose-dependent with resistance exercise in humans. The findings from this study represent the first indication that Akt activation is reduced in response to resistance exercise in human skeletal muscle, possibly to help mediate reductions in glycogen synthesis. / Human Performance Laboratory

The Major Intrinsic Proteins are represented in all forms of life; plants, animals, bacteria and recently archaebacteria have all been shown to express at least one member of this superfamily of integral membrane proteins. We have overexpressed the E. coli aquaglyceroporin, glycerol facilitator (GlpF), to use as a model for studying membrane protein structure, folding and stability. Understanding membrane protein folding, stability, and dynamics is required for a molecular explanation of membrane protein function and for the development of interventions for the hundreds of membrane protein folding diseases. X-ray analysis of GlpF crystals shows that the protein exits as a tetramer in the crystallized state [1]. However, preparations of stable aqueous detergent solutions of GlpF in its native oligomeric state have been difficult to make; the protein readily unfolds and forms non-specific aggregates in many detergents. Here, I report the study of the structure and stability of the glycerol facilitator in several detergent solutions by blue native and sodium dodecyl sulphate polyacrylamide gel electrophoresis, circular dichroism, and fluorescence. For the first time, stable protein tetramers were prepared in two different detergent solutions (dodecyl maltoside (DDM) and lyso-myristoyl phosphatidylcholine (LMPC)) at neutral pH. Thermal unfolding experiments show that the protein is slightly more stable in LMPC than in DDM and that the thermal stability of the helical core at 95oC is slightly greater in the former detergent. In addition, tertiary structure unfolds before quaternary and secondary structures in LMPC whereas unfolding is more cooperative in DDM. The high stability of the protein is also evident from the unfolding half-life of 8 days in 8 M urea suggesting that hydrophobic interactions contribute to the stability. The GlpF tetramers are less resistant to acidic conditions; LMPC-solubilized GlpF shows loss of tertiary and quaternary structure by pH 6, while in DDM the tertiary structure is lost by pH 5, however the tetramer remains mostly intact at pH 4. The implications of thermal and chemical stress on the stability of the detergent-solubilized protein and its in vivo folding are discussed.

Inducible chomosomal AmpC β-lactamase (AmpC) is present in many Gram-negative opportunistic human pathogens. Expressed in response to β-lactam antibiotics, AmpC is an enzyme that can deactivate an extended spectrum of β-lactam antibiotics and thereby promote bacterial survival. Inducible chromosomal ampC is associated with ampR, a gene that encodes a LysR-type transcriptional regulator that suppresses ampC expression in the absence of β-lactam exposure. Together, ampR and ampC form a divergent operon with overlapping promoters to which the AmpR protein binds and regulates the transcription of both genes. AmpR induces ampC expression by interacting with 1,6-anhydro-N-acetylmuramyl peptide, an intermediate of peptidoglycan recycling that is generated by a glycoside hydrolase encoded by nagZ. Given the role of NagZ and AmpR in the AmpC induction pathway, the structure and function of these proteins were investigated to understand the molecular basis for how they participate in AmpC production. The crystal structure of NagZ from Vibrio cholerae was determined in complex with the glycoside hydrolase inhibitor PUGNAc (O-(2-Deoxy-2-N-2-ethylbutyryl-D-glucopyranosylidene)amino-N-phenylcarbamate) to 1.8 Å resolution. Since PUGNAc also inhibits functionally related human enzymes, the structure of the enzyme was also determined in complex with the NagZ selective PUGNAc derivatives N-butyryl-PUGNAc (2.3 Å resolution) and N-valeryl-PUGNAc (2.4 Å resolution). These structural studies revealed the molecular basis for how 2-N-acyl derivatives of PUGNAc selectively inhibit the bacterial enzyme NagZ. The effector binding domain of AmpR from Citrobacter Spp. was determined to 1.83 Å resolution and lead to the identification of a putative effector molecule binding site. In vivo functional analysis of site directed mutants of AmpR containing amino acid substitutions at the base of the putative binding pocket verified its role in AmpR function. A protocol was subsequently devised to purify milligram quantities of soluble full-length AmpR. Biochemical and biophysical analysis, including non-denaturing mass spectrometry and small angle X-ray scattering, revealed that the purified full-length protein is tetrameric and specifically binds ampC promoter DNA. In summary, this research provides the basis for the development of small-molecules that could specifically block the activity of these proteins to suppress AmpC β-lactamase production during β-lactam therapy.

Previous experimentation using differential immunological screening identified Tp0326, a protein predicted to be located in the outer membrane (OM) of the bacterium Treponema pallidum. This protein is homologous to BamA members of the β-barrel assembly machinery (BAM) family of proteins, which are conserved throughout pathogenic Gram-negative bacteria. In Escherichia coli the BAM proteins are found as a complex composed of five proteins: BamA, which is an integral membrane protein, and four accessory lipoproteins, BamB - BamE, which localize to the inner leaflet of the outer membrane. In E. coli BamA has been shown to mediate the insertion and assembly of proteins in the OM via interaction with the BAM complex and periplasmic chaperones (SurA, Skp, and DegP). We hypothesize that a similar OMP translocation complex exists within T. pallidum and that this complex is responsible for ushering T. pallidum OMPs to the bacterial surface. Characterization of the putative T. pallidum OMP transport machinery was performed by bioinformatic analyses and protein-protein interaction studies. Protein-protein interaction studies included screening a T. pallidum Lambda genomic expression library with recombinant T. pallidum protein Tp0326 and Far-Western blotting techniques. Using bioinformatic analyses we have identified putative T. pallidum homologues of the E. coli lipoproteins BamD (Tp0622) and BamB (Tp0133) as well as putative homologues of the E. coli chaperone proteins Skp (Tp0327) and DegP (Tp0773). The T. pallidum Lambda genomic expression library screen identified the putative E. coli BamD homologue (Tp0622), which was originally discovered through bioinformatic analyses. The expression library screen also identified two putative T. pallidum OMPs (Tp0750 and Tp0751) as potential interaction partners of Tp0326. Combined bioinformatic analyses and protein-protein interaction studies provide evidence a BAM complex may exist within T. pallidum, and similar to E. coli, this complex may be involved in ushering T. pallidum OMPs to the bacterial surface. / Graduate

Proteins participate in the majority of cellular processes. To determine the function of a protein it is not sufficient to solely know its sequence, its structure in isolation, or how it works individually. Additionally, we need to know how the protein interacts with other proteins in biological networks. This is because most of the proteins perform their main function through interactions. This thesis sets out to improve the understanding of protein-protein interaction networks (PPINs). For this, we propose three approaches: (1) Studying measures and methods used in social and complex networks. The methods, measures, and properties of social networks allow us to gain an understanding of PPINs via the comparison of different types of network families. We studied models that describe social networks to see which models are useful in describing biological networks. We investigate the similarities and differences in terms of the network community profile and centrality measures. (2) Studying PPINs and their role in evolution. We are interested in the relationship of PPINs and the evolutionary changes between species. We investigate whether the centrality measures are correlated with the variability and similarity in orthologous proteins. (3) Studying protein features that are important to evaluate, classify, and predict interactions. Interactions can be classified according to different characteristics. One characteristic is the energy (that is the attraction or repulsion of the molecules) that occurs in interacting proteins. We identify which type of energy values contributes better to predicting PPIs. We argue that the number of energetic features and their contribution to the interactions can be a key factor in predicting transient and permanent interactions. Contributions of this thesis include: (1) We identified the best community sizes in PPINs. This finding will help to identify important groups of interacting proteins in order to better understand their particular interactions. We furthermore find that the generative model describing biological networks is very different from the model describing social networks A generative model is a model for randomly generating observable data. We showed that the best community size for PPINs is around ten, different from the best community size for social and complex network (around 100). We revealed differences in terms of the network community profile and correlations of centrality measures; (2) We outline a method to test correlation of centrality measures with the percentage of sequence similarity and evolutionary rate for orthologous proteins. We conjecture that a strong correlation exists. While not obtaining positive results for our data. Therefore, (3) we investigate a method to discriminate energetic features of protein interactions that in turn will improve the PPIN data. The use of multiple data sets makes possible to identify the energy values that are useful to classify interactions. For each data set, we performed Random Forest and Support Vector Machine with linear, polynomial, radial, and sigmoid kernels. The accuracy obtained in this analysis reinforces the idea that energetic features in the protein interface help to discriminate between transient and permanent interactions. / Graduate / 0984

Although integral membrane proteins represent nearly a quarter of the genes present in both prokaryotes and eukaryotes, progress in this area of research is often hindered due to the nature of their hydrophobic environment. Elucidating the folding pathway of these proteins is essential to understand many membrane mediated biological processes such as signal transduction, ion transport and chemotaxis. The wealth of structural and genetic information on bacteriorhodpsin renders it an ideal model system for the study of membrane proteins. Detailed studies however, necessitate efficient methods for its overexpression and purification. Previous expression systems have reported difficulty in obtaining good yields and simple purification procedures. This thesis investigates a variety of alternative expression and purification systems for the bacterio-opsin gene in Escherichia coli. With sufficient protein, site directed mutagenesis is performed to mutate three proline residues present in the membranous region of bacteriorhodopsin to alanine. The folding kinetics of these mutants is investigated using stopped flow fluorimetry to determine whether proline isomerisation is responsible for a slow step in the folding pathway of bacteriorhodopsin. Comparison of the results with those of the folding kinetics of wild type showed proline isomerisation not to be responsible for the slow step in the pathway. More recent studies have suggested that the slow step may be due to refolding conditions and lateral pressure the lipids impose upon the protein as well as pH. Separate structural studies using mass spectrometry aimed to study the rates of isotopic exchange of amide and side chain protons in bacteriorhodopsin. Low resolution results obtained using matrix assisted laser desorption ionisation mass spectrometry (MALDI-MS) prompted the investigation of electrospray ionisation mass spectrometry (ESI-MS). Techniques for sample preparation were optimised by investigating a variety of solvent systems and initial deuteration experiments performed.

No description available.

The mechanism of protein sorting to the vacuole in yeast was studied both in vitro and in vivo. A series of experiments were performed to reconstitute transport of carboxypeptidase Y (CPY) from Golgi vesicles to vacuoles. In order to investigate this process, microsomes were purified from sec, pep4-3 mutant strains that accumulate inactive proCPY in the Golgi when incubated at the nonpermissive temperature. These were mixed with purified vacuoles isolated from a mutant lacking CPY activity, but containing active proteinases A and B. Transported proCPY is maturated by these proteinases to active form. Experiments indicate that maturation of CPY is due to the correct transport of proCPY from microsomes to vacuoles because:- Firstly, the reaction is temperature sensitive, requires ATP and is stimulated by the addition of soluble factors (S100). Secondly, the addition of proteinase A and B inhibitors to the reaction mixtures has a negligible effect on the maturation process. Thirdly, disrupting the membranes by the addition of Triton X-100 before addition of the proteinase inhibitors, inhibited the maturation of proCPY. Fourthly, the majority of CPY activity was observed in the sedimented fraction of the reaction mixtures rather than supernatant fractions. Lastly, analysis with western blot shows a clear band of mature CPY only in the sedimented fraction of the reaction mixtures with ATP. This in vitro system will be invaluable in investigating the molecular events of vacuolar biogenesis. For in vivo sorting of proteins to the vacuole, a series of experiments were performed that involved the genetic fusion of the CPY promoter and prepro-sequence of CPY to the bacterial Gus (β-glucuronidase) reporter gene. The Gus gene was expressed in yeast with high efficiency and the results of sub-cellular fractionation indicated that the Gus product was distributed in all cell components. Using a centromeric vector gave similar results but with a lower efficiency of Gus expression. Removal of 90bp from Gus, including Gus initiation codon does not completely inhibit Gus expression either in bacteria or in yeast. Fusion of the shortened Gus with the CPY prepro-fragment and expression in yeast led to the correct sorting of the CPY-Gus hybrid protein to the vacuole. This CPY-Gus fusion is potentially useful in the genetic analysis of mutations defective in vacuolar protein sorting.

No description available.

No description available.