Submitted by Irene Nascimento (irene.kessia@ufpe.br) on 2016-10-04T19:09:24Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) tese mariana viana para BC revisado profa Rita.pdf: 5880006 bytes, checksum: 58b21f8952495e3aba8663b4efa5c48c (MD5) / Made available in DSpace on 2016-10-04T19:09:24Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) tese mariana viana para BC revisado profa Rita.pdf: 5880006 bytes, checksum: 58b21f8952495e3aba8663b4efa5c48c (MD5) Previous issue date: 2016-02-12 / Capes / O câncer de mama desenvolve-se de maneira silenciosa, podendo levar a óbito se não for tratado em sua fase inicial. Por este motivo, é necessário desenvolver técnicas para sua detecção precoce. A carcinogênese altera a temperatura dos tecidos na região afetada e o uso da simulação computacional calcula como ocorre tal fenômeno. A imagem por infravermelho é capaz de indicar a distribuição superficial de temperatura e a comparação destes valores com os cálculos obtidos na simulação computacional é uma ferramenta promissora para a detecção precoce do câncer de mama. O objetivo desta tese é construir a geometria substituta tridimensional (3D) da mama feminina a partir de imagens por infravermelho da paciente. Isso possibilita o cálculo da distribuição de temperatura através de software de dinâmica dos fluidos computacional (CFD – Computational Fluid Dynamics). O corregistro de uma prótese mamária externa aos contornos da paciente modelou a superfície da geometria tridimensional da mama. No interior dessa geometria existem os lóbulos mamários, os ductos lactíferos, o tecido adiposo da mama e a lesão conforme indicado no exame de ultrassonografia da paciente. Um software de CFD realizou o preparo da geometria e subsequente cálculo da distribuição de temperatura na mama. Um estudo de caso verificou o impacto da inserção das estruturas citadas na geometria substituta. O erro entre as temperaturas máximas indicadas pela imagem por infravermelho das pacientes na região da pele sobre a anomalia e a temperatura máxima alcançada no cálculo de temperatura sobre a região correspondente na geometria substituta foi de 0,20%. A geometria 3D aqui apresentada adequa-se aos contornos de cada paciente e é mais próxima da mama real do que a geometria substituta 3D obtida pelo escaneamento de próteses mamárias externas e outras apresentadas na literatura técnica. Além disso, a geometria desenvolvida permitiu o cálculo de temperatura nos casos em que não era possível com a geometria anteriormente utilizada. / Breast cancer develops silently and can lead to death if not treated in its early stages. For this reason, it is necessary to develop techniques for its early detection. The carcinogenesis changes the temperature of the tissue in the affected area, the use of computer simulation to evaluate how such a phenomenon occurs. The infrared image can indicate the surface temperature distribution, and the comparison of these figures with the calculations obtained in a computer simulation is a promising tool for early detection of breast cancer. The purpose of this thesis is to build three-dimensional (3D) surrogate geometry of the female breast from infrared images of the patient. It allows the calculation of the distribution of temperature through Computational Fluid Dynamics (CFD) software. The breast prosthesis co-registration to the contours of the patient modeled the external surface of the 3D geometry of the breast. Within this geometry, there are mammary lobules, lactiferous ducts and adipose tissue of the breast and the lesion as indicated in the ultrasound examination of the patient. CFD software performed the preparation of the geometry and subsequent calculation of the breast temperature distribution. A case study verified the impact of the insertion of such structures in the surrogate geometry. The error between the maximum temperature indicated by the infrared image of the patient in the area of the skin over the abnormality and the maximum temperature achieved in the temperature calculation in the corresponding region in the surrogate geometry were 0.20%. The 3D geometry presented here fits the contours of each patient, and it is closer to the real breast than the surrogate 3D geometries acquired by the scanning of external breast prostheses and others ones presented in the technical literature. Furthermore, the modeled geometry allowed the temperature calculation in cases where it was not possible with the geometry that was previously used.

Submitted in the fulfillment of the requirement for the Degree of Master's in Chemistry, Durban University of Technology, 2017. / P53 is a tumour suppressor protein that is dysfunctional in most human cancer cells. Mutations in the p53 genes result in the expression of mutant proteins which accumulate to high levels in tumour cells. Several studies have shown that majority of the mutations are concentrated in the DNA-binding domain where they destabilize its conformation and eliminate the sequence- specific DNA-binding to abolish p53 transcription activities. Accordingly, this study involved an investigation of the effects of mutations associated with cancer, based on the framework of sequences and structures of p53 DNA-binding domains, analysed by SIFT, Pmut, I-mutant, MuStab, CUPSAT, EASY-MM and SDM servers. These analyses suggest that 156 mutations may be associated with cancer, and may result in protein malfunction, including the experimentally validated mutations. Thereafter, 54 mutations were further classified as disease- causing mutations and probably have a significant impact on the stability of the structure. The detailed stability analyses revealed that Val143Asp, Ala159Pro, Val197Pro, Tyr234Pro, Cys238Pro, Gly262Pro and Cys275Pro mutations caused the highest destabilization of the structure thus leading to malfunctioning of the protein. Additionally, the structural and functional consequences of the resulting highly destabilizing mutations were explored further using molecular docking and molecular dynamics simulations. Molecular docking results revealed that the p53 DNA-binding domain loses its stability and abrogates the specific DNA-binding as shown by a decrease in binding affinity characterized by the ZRANK scores. This result was confirmed by the residues Val143Asp, Ala159Pro, Val197Pro, Tyr234Pro and Cys238Pro p53-DNA mutant complexes inducing the loss of important hydrogen bonds, and introduced non-native hydrogen bonds between the two biomolecules. Furthermore, Molecular dynamics (MD) simulations of the experimental mutant forms showed that the structures of the p53 DNA-binding domains were more rigid comparing to the wild-type structure. The MD trajectories of Val134Ala, Arg213Gly and Gly245Ser DNA-binding domain mutants clearly revealed a loss of the flexibility and stability by the structures. This might affect the structural conformation and interfere with the interaction to DNA. Understanding the effects of mutations associated with cancer at a molecular level will be helpful in designing new therapeutics for cancer diseases. / M

This work discusses applications of computational simulations to enzymatic systems with a particular focus on the effects of various small perturbations on cancer and disease-related systems. First, we cover the development of carbohydrate-based PET imaging ligands for Galectin-3, which is a protein overexpressed in pancreatic cancer tumors. We uncover several structural features for the ligands that can be used to improve their binding and efficacy. Second, we discuss the AlkB family of enzymes. AlkB is the E. coli DNA repair protein for alkylation damage, and has human homologues with slightly different functions and substrates. Each has a conserved active site with a catalytic iron and a coordinating His...His...Asp triad. We have applied molecular dynamics (MD) to investigate the effect of a novel single nucleotide polymorphism for AlkBH7, which is correlated with prostate cancer and has an unknown function. We show that the mutation leads to active site distortion, which has been confirmed by experiments. Thirdly, we investigate the unfolding of hen egg white lysozyme in 90% ethanol solution and low pH, to show the initial steps of unfolding from a native-like state to the disease-associated beta-sheet structure. We compare to mass spectrometry experiments and also show differing pathways based on protonation state. Finally, we discuss three different DNA polymerase systems. DNA polymerases are the primary proteins that replicate DNA during cell division, and have various extra or specific functions. We look at a proofreading-deficient DNA polymerase III mutant, the effects of solvent on DNA polymerase IV's ability to bypass bulky DNA adducts, and a variety of mutations on DNA polymerase kappa.