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Bioinformatics Tool for the Design of Disulfide Bonds in Protein Structure
Sumbalová, Lenka ; Burgetová, Ivana (referee) ; Martínek, Tomáš (advisor)
Proteins are substances with great usage. For industrial usage, proteins are often taken from their natural enviroment. In foreign environment, it proteins can unfold and their function can be compromised. This is the reason for stabilization of proteins and one of ways to stabilization is using disulphide bonds. This work describes basic terms related to protein stabilization - proteins, their structure and interactions within them, basic terms from thermodynamics. Problem of protein stability is discussed and the factors which stabilize or destabilize protein are enumerated with the emphasis on disulphide bonds. Existing approaches to disulphide bonds design, dataset for testing own tool are described. Implementation of the tool using geometrical properties of the bonds and fl exibility of places in protein is described. The tool was tested on proteins with native disulfide bonds and compared to existing tools, also metrics FRO (fractional rank order) was used. Native disulfide bond was found in 64 % of cases, in 60 % of cases this native disulfi de bond was in the first quarter of ordered found disulfi de bonds.
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Preparation of a new insulin analog in order to study the interaction of the hormone with insulin receptor isoforms,
Halamová, Tereza ; Jiráček, Jiří (advisor) ; Obšilová, Veronika (referee)
Insulin acts as a key hormone in the blood glucose levels maintaining mechanisms. Outside this metabolic function it also has a growth hormone functionality. The interaction of insulin with the two existing insulin receptor isoforms - IR-A and IR-B, which are variously represented in the human body is determining insulin. IR-A, supposed to be mainly responsible for the mitogenic function of insulin, is located in the brain or lymphatic cancer and fetal tissue, whereas IR-B, performing metabolic function is located in adipose and muscle tissue. Present aim is to design such insulin analogs that would preferentially bind to IR-B, and could thus more efficiently carry out physiological metabolic function of insulin necessary for patients with diabetes. Based on the recently solved 3D structure of insulin bound to IR, it was found that the C-terminus of the B-chain of insulin must undergo conformational change bending it in about 90ř, for efficient binding to IR. The aim of this thesis was the preparation and characterization of two insulin analogs with bridging C-terminus of the B-chain in positions B26-B29 and B27-B29 using disulfide bridge. This could fix a bended structure of the B chain end and could help to increase the affinity of IR and specificity for IR-B. The preparation was carried out...
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Bioinformatics Tool for the Design of Disulfide Bonds in Protein Structure
Sumbalová, Lenka ; Burgetová, Ivana (referee) ; Martínek, Tomáš (advisor)
Proteins are substances with great usage. For industrial usage, proteins are often taken from their natural enviroment. In foreign environment, it proteins can unfold and their function can be compromised. This is the reason for stabilization of proteins and one of ways to stabilization is using disulphide bonds. This work describes basic terms related to protein stabilization - proteins, their structure and interactions within them, basic terms from thermodynamics. Problem of protein stability is discussed and the factors which stabilize or destabilize protein are enumerated with the emphasis on disulphide bonds. Existing approaches to disulphide bonds design, dataset for testing own tool are described. Implementation of the tool using geometrical properties of the bonds and fl exibility of places in protein is described. The tool was tested on proteins with native disulfide bonds and compared to existing tools, also metrics FRO (fractional rank order) was used. Native disulfide bond was found in 64 % of cases, in 60 % of cases this native disulfi de bond was in the first quarter of ordered found disulfi de bonds.
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