Thesis (Ph.D.) -- University of Texas Southwestern Medical Center at Dallas, 2006. / Embargoed. Vita. Bibliography: 93-99.

Thesis (Ph. D.)--University of Missouri-Columbia, 2006. / The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Vita. "August 2006" Includes bibliographical references.

Thesis (Ph. D.)--Virginia Commonwealth University, 2006. / Prepared for: Dept. of Microbiology and Immunology. Bibliography: leaves 134-165.

In this dissertation,the membrane protein channelrhodopsin-1 from the green flagellate algae Chlamydomonas agustae (CaChR1) is studied using a variety of spectroscopic techniques developed in the Rothschild Molecular Biophysics Laboratory at Boston University. Over the last decade, channelrhodopsins have proven to be effective optogenetic tools due to their ability to function as light-gated ion channels when expressed in neurons. This ability allows neuroscientists to optically activate an inward directed photocurrent which depolarizes the neuronal membranes and triggers an action potential. Although a variety of channelrhodopsins with different properties have been used, the underlying mechanisms of channelrhodopsin functionality is not yet fully understood. The protein studied here has several advantageous properties compared to the more extensively studied channelrhodopsin-2 from Chlamydomonas reinhardtii including a red shifted visible absorption and slower light inactivation despite having a lower channel current. Elucidating the internal molecular mechanisms underlying the function of CaChR1 provides critical insight into the large class of channelrhodopsin proteins leading toward improved bioengineering for specific optogenetic applications. Here near-IR pre-resonance Raman spectroscopy of CaChR1 provides information on the structure of the unphotolyzed (P0) retinal chromophore, the Schiff base protonation state, and presence of carboxylic acid residues interacting with the Schiff base. Low-temperature FTIR difference spectroscopy combined with site-directed mutagenesis and isotope labeling provide information on changes occurring in the retinal chromophore and protein during the primary phototransition (P0 to P1). This includes information about changes involving protonation state of binding-pocket residues, protein backbone structure, and internal water molecules. Further experiments combining low-temperature and time-resolved FTIR-difference spectroscopy reveal additional information about structural changes during the transition from the unphotolyzed state to the active (open channel) state of the protein (P0 to P2). This work has resulted in an initial model that describes key proton transfer events which occur between the Schiff base and carboxylic acid residues inside the active site of CaChR1. The model raises the possibility that ion channel gating and ion specificity is regulated by the protonation changes of two key residues (Glu 169 and Asp299) located near the Schiff base.

No description available.

The cytoplasmic surface of Sec61p is the binding site for the ribosome and has been proposed to interact with the signal recognition particle receptor during targeting of the ribosome nascent chain complex to the translocation channel. Point mutations in cytoplasmic loops six (L6) and eight (L8) of yeast Sec61p cause reductions in growth rates and defects in translocation of nascent polypeptides that utilize the cotranslational translocation pathway. Sec61 heterotrimers isolated from the L8 sec61 mutants have a greatly reduced affinity for 80S ribosomes. Cytoplasmic accumulation of protein precursors demonstrates that the initial contact between the large ribosomal subunit and the Sec61 complex is important for efficient insertion of a nascent polypeptide into the translocation pore. In contrast, point mutations in L6 of Sec61p inhibit cotranslational translocation without significantly reducing the ribosome binding activity, indicating that the L6 and L8 sec61 mutants impact different steps in the cotranslational translocation pathway. Integral membrane proteins are cotranslationally inserted into the endoplasmic reticulum via the protein translocation channel, which mediates the translocation of lumenal domains, retention of cytosolic domains and integration of transmembrane spans into the phospholipid bilayer. We analyzed the in vivo kinetics of integration of model membrane proteins in Saccharomyces cerevisiae using ubiquitin translocation assay reporters. A signal anchor sequence from a type II membrane protein gates the translocon pore less rapidly than a cleavable signal sequence from a secretory protein. Transmembrane spans and lumenal domains are exposed to the cytosol during integration of a poly topic membrane protein. The conformational changes in the translocon that permit opening of the lumenal and lateral channel gates occur less rapidly than elongation of the nascent polypeptide. Cytosolic exposure of transmembrane spans and lumenal domains poses a challenge to the fidelity of membrane protein integration.

Foram estudadas as proteínas da membrana eritrocitária de quarenta e seis espécies diferentes pertencentes à treze ordens da classe Mammalia, através de eletroforese em gel de poliacrilamida. Observamos que: 1. não parece haver correlação entre as concentrações relativas de espectrinas e o volume corpuscular médio. 2. não parece haver correlação entre as concentrações relativas de banda 3 e o volume corpuscular médio. 3. parece haver uma correlação inversa entre as concentrações relativas das anquirinas e o volume corpuscular médio. Assim, a maior parte dos animais pertencentes à ordem dos Artiodacty/a estudados (girafa, cervo nobre, veado campeiro, veado catingueiro, carneiro, cabra), que apresentam volume corpuscular baixo, exibe aumento significativo da concentração das anquirinas. 4. observou-se, o aparecimento de uma banda difusa na região 4.5 no Didelphis marsupialis (gambá), Arctocephalus tropicalis e Arctocephalus australis (lobo marinho subantártico e lobo marinho das ilhas do sul) e Panthera leo (leão) quando os estromas são submetidos à ação do NEM na concentração de 200 µM, e o não encontro desta banda nas demais espécies estudadas. Este fato poderia advir da hipótese de haver, nas três espécies, sequências de aminoácidos comuns que possibilitariam a ação química direta do NEM. 5. observou-se que, nos mamíferos estudados, embora houvesse variações qualitativas e quantitativas das proteínas da membrana nas espécies estudadas, práticamente todas elas apresentaram as proteínas descritas no Homo sapiens, mostrando serem todas elas importantes na manutenção do citoesqueleto e da membrana como um todo. 6. Com exceção da cutia, que exibe provavelmente quatro formas de espectrinas, todas as demais espécies exibiram duas formas, embora com variações qualitativas e quantitativas. 7. A banda 3 foi a proteína que mais exibiu variação, seja no peso molecular, com variação desde 95 kDa (Capra hircus, cabra) até 169 kDa (Alouatta sp, bugio), seja no aspecto difuso ou bem definido. 8. Houve na região 4.1/4.2 uma variabilidade grande, seja qualitativa, seja quantitativa com aparentes ausências dê\' uma ou de outra. Alguns roedores, a cobaia, cutia, hamster exibiram somente uma banda protéica na região 4.1/4.2. 9. Entre os primatas, todas as proteínas apresentaram o mesmo padrão entre os Hominoidea (macacos antropóides, Gorilla gorilla e Pongo pygmaeus e homem, Homo sapiens) e os do Velho Mundo (Cercopithecoidea, Papio cynocephalus e Erythrocebus pata). Mas, os primatas do Novo Mundo (Ceboidea, Cebus apella, Alouatta sp e AteIes paniscus chamek) apresentaram variação do peso molecular da banda 3, apresentando no entanto o mesmo aspecto difuso dos outros primatas descritos anteriormente. 10. Com exceção do Didelphis marsupialis (gambá) e Giraffa came/opardalis (girafa), que apresentaram evidência da ação de serina-proteases sobre uma anquirina, as demais espécies não exibiram proteases intra-eritrocitárias ativas nas condições estudadas. / Forty six different mammal species from thirteen regarding their erythrocyte membrane proteins, following data were observed: 1. No correlation was observed between mean corpuscular volume and spectrins concentration. 2. No correlation was observed between mean corpuscular volume and band 3 concentration. 3. It seems that there is inverse correlation between mean corpuscular volume and ankyrins concentration. Most of the studied animmals belonging to Artiodactyla, which exhibit low mean corpuscular volume, present higher ankyrin concentration. 4. A diffuse band in 4.5 region was observed among the Didelphis marsupialis, Arctocephalus tropicalis, Arctocephalus australis and Panthera leo when the ghosts were treated with 200 µM NEM, what was not found in the others species. This fact could be ascribed to hypothetical sequence of the Iysine, hystidine and cysteine which may be prone to NEM direct chemical action. 5. Although some qualitative and quantitative changes were observed among ali the studied species, ali of them seem to occur in the humans, disclosing that they are \"house-keeping\" proteins which participate as important pieces in the cytoskeleton structure and the membrane as well. 6. Ali the species presented two spectrins, with exception of Dasyprocta sp., which exhibited fours bands in the spectrins region. 7. The band 3 was the protein which showed the greatest variation, since 95 kDa in the Capra hircus up to 169 kDa in the Alouatta sp., as well as in the aspect, diffuse or well defined. 8. A great variability was observed in the 4.1/4.2 region, with apparent absence of one or another. Some Rodentia exhibited only one protein in the 4.1/4.2 region. 9. Among the Primates, the Hominoidea and the Cercopithecoidea presented an uniform pattern, but the New World monkeys (Cebus apella, Alouatta sp. and Ateies paniscus chamek) exhibited a striking molecular weight band 3 variation, although keeping the common diffuse pattern. 11. Ali the studied species did not present the evidence of protease action upon the membrane proteins, except the Didelphis marsupialis and Giraffa camelopardalis, which disclosed a proteolytic action upon the ankyrin.

We have developed a new approach for locating transmembrane domains in protein sequences based on hydrophobicity analysis and backpropagation neural network or k-nearest-neighbor as classifiers. Our system was able to locate over 98% of the transmembrane domains and the total accuracy including overpredictions was above 95%.

Abstract Anion exchanger 2 (AE2) is a member of the anion exchanger gene family, which includes three additional members, AE1, AE3, and AE4. They are also known as Na+-independent Cl-/HCO3- exchangers, and their major function is to regulate intracellular pH and chloride concentration. All four isoforms have several N-terminally truncated variants that are often expressed cell type specifically. Red blood cells express the full-length AE1 isoform that interacts with ankyrin, an adapter protein linking plasma membrane to the spectrin-based membrane skeleton. This membrane skeleton association is essential for maintaining the membrane integrity of red blood cells. AE3 variants are mainly found in the brain and heart, whereas AE4 is localized in the kidney. Anion exchanger 2 is expressed in every cell line and tissue studied thus far, and it has been mainly localized to the plasma membrane. However, we found two types of localization/targeting of the AE2 protein in several of the cell lines studied. The protein was localized to either the plasma membrane or the Golgi complex, depending on the cell type. The AE2 variant expressed in these cells was identified as the full-length AE2 protein. The determinants of differential intracellular targeting were assessed. We hypothesized that Golgi-AE2 is anchored to the Golgi membranes via its association with the Golgi membrane skeleton. We were able to show that the Golgi localization of AE2 correlated with the cell type specific expression of Ank195, a Golgi membrane skeletal protein. In cells where AE2 was targeted to the plasma membrane, Ank195 was not expressed. In addition, the detergent insolubility and co-redistribution properties of AE2 and Ank195 strongly suggested that these proteins interact with each other. The Golgi membrane skeleton has been shown to be necessary for maintaining the Golgi structure. Our studies were consistent with these findings, showing that in cells in which AE2 expression was reduced by using AE2-specific antisense oligonucleotides, the Golgi complex was dispersed. The spectrin-based membrane skeleton was probably partially detached from the Golgi membranes leading to breakdown of the Golgi structure and disorganization of the microtubules associated with it. The present findings suggest that the targeting of AE2 is cell type specific, and that Golgi-localized AE2 serves as a membrane association site for the spectrin-based Golgi membrane skeleton, thereby participating in the maintenance of the Golgi structure.

Magister Scientiae (Medical Bioscience) - MSc(MBS) / Passage of spermatozoa through the female reproductive tract is essential for the regulation of fertilization, ensuring that healthy sperm reach the oocyte. Previous studies were devoted to morphological selection of sperm cells by the cervical mucus. However, research prove that the loss of integrity of the sperm plasma membrane is associated with infertile men, irrespective of their normal semen parameters. This indicates that the sperm plasma membrane plays an important role in fertilization. Further studies indicated that sperm surface proteins assist penetration through the female reproductive tract and would therefore provide useful insight in understanding other factors associated with male infertility. The aim of this project was to determine if there are any differences between sperm surface proteins of fertile donor samples in relation to infertile patient samples using different separation techniques and different detergents. Three different sperm separation techniques were employed, including wash, swim-up (SU) and Percoll density gradient centrifugation (DGC).Parallel to this, the deoxy-ribose nucleic acid (DNA) fragmentation of these cells were analysed for comparison of the extent of DNA damage induced due to different separation techniques used. This provided evidence that the best separation technique is the DGC as it minimises the amount of DNA fragmentation caused. Four different detergents were used in the process of extracting the membrane proteins from spermatozoa, namely sodium dodecyl sulphate (SDS), saponin,cetyl-trimethyl-ammonium bromide (CTAB), and TWEEN-20. The membrane proteins were then separated on a12% SDS poly-acrylamide gel electrophoresis (PAGE), and analysed by Coomassie blue and silver staining techniques as well as densitometry. Due to the different chemical nature of the detergents that extracted different surface proteins, CTAB (cationic) and SDS (anionic) extracted the most because of its strong solubilising abilities as non-ionic detergents. Common proteins that were extracted in donor samples included; 115, 92.5, 89, 61, 55.5, 51.5, 47, 44.5, 43, 38.5, 34 and 28 kDa proteins. In patients, commonly occurring proteins included; 92.5, 74.5, 70, 60.5, 51.5, 50, 44.5, 43, 36, 29.5, and 25.5 kDa proteins. Marked differences were found between membrane proteins extracted from donor samples in comparison to patient samples. Identification of these proteins was done using the SwissProt database and a literature search. Mostly non-genomic progesterone receptors were identified; others included oestrogen receptor, a phosphotyrosyl protein, P34H, equatorial segment protein, mannose lectin receptor, human guanylylcyclase receptor, epididymal protease inhibitor receptor, PH30 and estradiol binding protein. The function of the membrane surface proteins identified in this study plays a vital role in fertilization. A few of these functions include sperm attachment and binding to the oocyte as well as penetration thereof. Others play a role in signalling events such as capacitation, hyperactivation and acrosome reaction. The absence of these proteins in patient sperm possibly accounts for the functional inability to successfully achieve fertilization suggesting that this provides molecular insight to reasons for infertility amongst men. In addition to this, proteins presented by patient samples that were absent in healthy donors may too account for their infertility status. Estradiol binding protein and PH30 are two proteins presented only in patient samples. Their function plays a role in the inhibition of the acrosome reaction and sperm-egg fusion, respectively. In conclusion, these differences in protein expression between fertile donors and patients may form the molecular basis of infertility amongst men and indicates possibilities for novel proteonomic approaches to improve andrological diagnosis in future.