A neutral calcium-activated protease of muscle (CAP) has previously been characterised and may play a role in myofibrillar disassembly and turnover. In this study both CAP and endogenous CAP inhibitor from adult and embryonic chicken skeletal muscle have been partially purified by DEAE-cellulose and Sephadex G-150 chromatography. CAP from embryonic muscle shows similar properties to the corresponding enzyme from adult tissue with respect to calcium dependence (maximum activity at 1.0 rnM Ca²⁺), pH optimum (7.2) and sensitivity to proteinase inhibitors (inhibited by leupeptin and chymostatin). Both embryonic and adult enzymes were found to have molecular weights of 112000 daltons by gel filtration on Sephadex G-150. CAP activity was present in cultured skeletal muscle cells and increased with cellular growth and differentiation (five-fold). The presence of an inhibitor of CAP was demonstrated in cell cultures by ion-exchange chromatography, the levels of which decreased with a simultaneous increase in CAP activity. CAP activity showed an increase in developing muscle from 12-day embryos to 7-week chicks in relation to cellular DNA (3.8- fold), although the extent of this increase did not match the extent of accumulation of myofibrillar proteins. High levels of CAP inhibitor were found in early embryonic muscle and these decreased markedly during development. CAP inhibitor from embryonic tissue was fractionated into 3 species using DEAE-cellulose in contrast to inhibitor from adult tissue which exhibited only two species. The results indicate that the levels of CAP greatly increase at a time when myofibrillar content of muscle is rapidly increasing and, in addition, demonstrate that CAP activity may be controlled to a large extent by the levels of an intracellular inhibitor.

FrpC protein produced by Neisseria meningitidis in a human host belongs to the family of bacterial RTX toxins due to the presence of RTX domain. FrpC possesses a calcium-dependent auto-catalytic cleavage activity which is localized within its 177 amino-acids long segment Self-Processing Module (SPM). As the SPM is naturally intrinsically disordered protein without bound Ca2+, the calcium binding is crucial for SPM folding which is followed by the auto-catalytic processing. The elucidation of the SPM structure may be the key step for understanding of enzymatic and biological function. The structure of folded SPM itself can be characterized only with difficulties due to the presence of flexible loop according to preliminary NMR data. The subject of this work is the description of SPM using fluorescence methods, characterization of ions binding to SPM and structural changes occurring during Ca2+ binding. In this work, the ion binding properties of SPM segment and its ion-induced folding was characterized. It was found that the dissociation constant kD of 17 μM coincided with the folding of SPM into the native calcium-bound state which occurs in the concentration range between 1 and 20 μM Ca2+. In the attempt to characterize the structure of ion binding site, the fully active single tryptophan mutants...

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by Au Ka Wing. / "June 2004." / Thesis (Ph.D.)--Chinese University of Hong Kong, 2004. / Includes bibliographical references (p. 153-162). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Mode of access: World Wide Web. / Abstracts in English and Chinese.

Orientador: Pedro de Magalhães Padilha / Coorientador: Luís Artur Loyola Charduto / Banca: Luciana Francisco Fleury / Banca: Angélica Simone Cravo Pereira / Resumo: O presente trabalho retrata estudo metaloproteômico no tecido muscular de bovinos da raça Nelore (Bos indicus) contrastantes para a característica de maciez da carne baseado em métodos de separação de proteínas por eletroforese bidimensional (2D-PAGE), identificação dos íons cálcio nos spots proteicos por fluorescência de raio-X (SR-XRF) e caracterização das proteínas por espectrometria de massas (ESI-MS). Os animais selecionados para compor o grupo M (carne macia) expressaram valores de força de cisalhamento (FC) entre 3,39 e 3,98 kg, já os animais selecionados para o grupo D (carne dura) expressaram valores de FC entre 7,11 e 7,45 kg. Foi incluído um terceiro grupo (P) de animais da raça Piemontês (Bos taurus) como modelo comparativo do grau de maciez da carne. O número médio de spots proteicos encontrados nas repetições dos géis dos grupos M, D e P foram de 186 ± 20, 146,5 ± 16,5 e 175 ± 15, respectivamente. As correlações obtidas nas repetições dos géis indicaram que os procedimentos de extração da proteína total foram eficientes e preservaram a estrutura metal-proteína. A maior detecção (56%) qualitativa de cálcio por SR-XRF nos spots proteicos de animais com carne macia é um indicativo da ocorrência da atividade proteolítica no tecido muscular durante o período post mortem. A 2D-PAGE foi eficiente no fracionamento das proteínas presentes em amostras de tecido muscular (Longissimus dorsi). As correlações obtidas nas repetições dos géis indicaram que os procedimentos de extração da proteína total foram eficientes e preservaram a estrutura metal-proteína / Abstract: The present article describes a metalloproteomics study of bovine muscle tissue with different grades of meat tenderness from animals of the Nellore breed (Bos indicus) based on protein separation by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), the identification of calcium ions in protein spots by Synchrotron Radiation X-ray Fluorescence (SR-XRF) and the characterization of proteins by electrospray ionization mass spectrometry (ESI-MS). The meat from the animals selected to form the Te group (tender meat) expressed shear force (SF) values ranging from 3.39 to 3.98 kg, and the meat from the animals selected for the To group (tough meat) expressed values ranging from SF 7.11 to 7.45 kg. A third group (P) of Piedmontese animals (Bos taurus) was included as a comparative model for the level of meat tenderness. The mean number of protein spots found in the gel replicates of the Te, To and P groups were 186 ± 20, 146.5 ± 16.5 and 175 ± 15, respectively. The correlations found in the gel replicates indicated that the total protein extraction procedures were efficient and preserved the metal-protein structure. The higher qualitative detection of calcium (56%) by SR-XRF in the protein spots of animals with tender meat was indicative of the occurrence of proteolytic activity in the muscle tissue during the post mortem period. The 2D-PAGE was efficient fractionation of proteins present in muscle tissue samples (Longissimus dorsi). The correlations obtained in repetitions of the gels indicated that the procedures for extraction of total protein were efficient and preserved the structure metal-protein / Mestre

Most questions in proteomics require complex answers. Yet graph theory, supervised learning, and statistical model have decomposed complex questions into simple questions with simple answers. The expertise in the field of protein study often address tasks that demand answers as complex as the questions. Such complex answers may consist of multiple factors that must be weighed against each other to arrive at a globally satisfactory and consistent solution to the question. In the prediction of calcium binding in proteins, we construct a global oxygen contact graph of a protein, then apply a graph algorithm to find oxygen clusters with the fixed size of four, finally employ a geometry algorithm to judge if the oxygen clusters are calcium-binding sites or not. Additionally, we can predict the locations of those sites. Furthermore, we construct a global oxygen contact graph including oxygen-bonded carbon atoms of a protein, then apply a graph algorithm to find local biggest oxygen clusters, finally design another geometric filter to exclude the non-calcium binding oxygen clusters. In addition, we apply observed chemical properties as a chemical filter to recognize some non-calcium binding oxygen clusters. In order to explore the characteristics of calcium-binding sites in proteins, we conduct a statistic survey on four datasets derived from 1994 to 2005 about the geometric parameters and chemical properties of calcium-binding sites. In the prediction of disulfide bond connectivity, we analyze protein sequences to predict the folding of proteins relative to the cystines using nearest neighboring methods. we extend a new pattern-wise method to all available template proteins, and find global pattern of pairing cysteines with a new descriptor of cysteine separation profile on protein secondary structure.

Thesis (Ph. D.)--West Virginia University, 2002. / Title from document title page. Document formatted into pages; contains xiii, 134 p. : ill. (some col.). Vita. Includes abstract. Includes bibliographical references (p. 119-128).

Thesis (Ph. D.)--University of Washington, 2001. / Vita. Includes bibliographical references (leaves 86-89).

Transient change of cytosolic calcium level leads to physiological actions, which are modulated by the intracellular calcium stores, and gated by membrane calcium channels/pumps. To closely monitor calcium dynamics there is a pressing need to develop calcium sensors that are targeted to high calcium environment such as the ER/SR with relatively low binding affinity and fast kinetic properties to complement the current calcium indicator toolkits. In this dissertation, the development of fast red florescent calcium binding protein using the protein design is reported. The results show the calcium dependent fluorescence increase of mCherry mutant MCD1 (RapidER) and MCD15 (RapidER’) is able to monitor the ER calcium release in several cell lines responding to perturbations of extracellular calcium signaling. The specific targeting to the ER membrane was achieved by fusing the ryanodine receptor 1 transmembrane domains for the spatio-temporal calcium imaging. To understand the underlying mechanism of calcium binding induced fluorescence increase in the designed calcium sensor CatchER, the fluorescence lifetime of CatchER was determined in calcium free and bound forms using time resolved florescence spectroscopy. The results suggest that calcium binding inhibits the geminate quenching, resulting in a longer lifetime when the anionic form is indirectly excited at 395 nm. It is believed that such unique calcium-induced lifetime change can be applied to monitor calcium signaling in cell imaging. NMR spectroscopy was used to investigate the protein-protein/ligand interaction in this dissertation. The residual dipolar coupling and T1, T2, NOE dynamic study were carried out to understand the binding mode of CaM and the N-terminal intracellular loop of connexin 43. The results show that both N and C terminal domains of Ca2+-CaM contact with the peptide, leading to a partially unwound and bending central helix of CaM. The ligand binding induced conformational change was demonstrated by selectively labeled proteins including extracellular domain of calcium sensing receptor and the bacterial membrane protein SecA fragments C34 and N68.