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.

Genomic integrity is important for living cells' correct functioning and propagation. Deoxyribonucleic acid as a molecule is a subject to chemical reactions with agents that can come from environment as well as from internal metabolism processes. These reactions can induce damage to DNA and thus compromise the genetic information, and result in disease and death of an organism. To mitigate the damage to DNA, cells have evolved to have multiple DNA repair pathways. Presented here is a computational study of DNA repair genes. The structure of the Homo sapiens direct DNA repair gene ALKBH1 is predicted utilizing homology modeling methods and using AlkB and DBL proteins as templates. Analysis of the obtained structure and molecular dynamics simulations give insights into potentially functionally important residues of the protein. In particular, zinc finger domains are predicted, and lysines that could perform catalytic activities are investigated. Subsequent mutagenesis experiments revealed the effect of the residues predicted to form zinc fingers on activity of ALKBH1. Structure and dynamics of AlkD, a Bascillus cereus base excision DNA repair protein is also studied. This protein has been shown to bind DNA with large alkyl adducts and perform excision catalysis without base flipping which is characteristic to other enzymes in the same family. MD simulations of AlkD revealed that B helix, which interacts with DNA, has higher fluctuations when AlkD is not bound to DNA, and thus could have a role in binding and recognition of DNA. For the purpose of finding biomarkers and to further our understanding of a mode of action of DNA repair genes, statistical methods were applied to identify mutations that are linked to cancer phenotypes. Analysis was based on case-control studies of patients with cancers of prostate, breast, pancreas, lung as well as chronic lymphocytic leukemia from NCBI dbGAP database. Those mutations that result in missense mutations were further investigated. In particular, extensive MD simulations and experimental investigations were performed on the mutation in the ALKBH7 gene that was found to be linked to prostate cancer.