title: Assessing functional impact of amino acid alterations in proteins
creator: Gonzalez Sanchez, Juan Carlos
subject: ddc-004
subject: 004 Data processing Computer science
subject: ddc-500
subject: 500 Natural sciences and mathematics
subject: ddc-570
subject: 570 Life sciences
description: Genome sequencing efforts, coupled with technological advances and cost reductions, have led to the discovery of an increasing number of disease-related genetic variants. For the vast majority of these variants there is no known molecular mechanism for how they are related to the disease. This problem is particularly evident for diseases with complex genotype-phenotype relationships, such as cancer. Fortunately, the parallel growth of data on protein families, structures, interactions, modifications, and other aspects of function, in addition to the development of new computational methods provide the means to predict or identify disease variant mechanism.  In this thesis, I first present a systematic analysis of a large dataset of pan-cancer missense mutations to investigate whether positive selection of certain types of amino acid substitutions can reveal interaction-disrupting cancer driver mutations. Hundreds of mechanistically interesting variants were identified in both potentially novel cancer-associated proteins and well-established cancer driver genes. I discuss new insights and for some instances, attempt functional interpretations by integrating information on protein structure and interactions that suggest putative novel mechanisms that question the classical oncogene/tumour suppressor paradigm.  There is a wealth of publicly available resources that already provide valuable information on all aspects that define gene and protein function. This information has been collected from thousands of experiments or publications and has usually been manually verified or predicted using new approaches. This means that interpreting variants can be a tedious process of manually consulting and integrating the different functional data from multiple databases. Mechnetor was developed to aid this process: a freely available web tool that helps users understand the mechanism of protein variants. With a simple input from the user, Mechnetor automatically collects and integrates various relevant functional data and presents them in an interactive network that allows easy visualisation and interpretation of the results.  Many databases are created from the individual efforts of hundreds of labs conducting similar experiments, combining their results to build and increase the confidence of biological knowledge. I had the opportunity to collaborate with the group of Prof. Dr. Felix iv  Wieland (Heidelberg University Biochemistry Center) in analysing and interpreting the results of one such experiment: a proteome-wide study of S-palmitoylation in Drosophila melanogaster. S-palmitoylation is an important reversible post-translational modification that controls protein membrane location and trafficking and is thus linked to many cellular processes. In contrast to humans, palmitoylation target proteins and responsible enzymes are largely unknown in invertebrates. Here, we identified and characterised the most complete set of S-palmitoylated proteins in Drosophila to date, as well as the putative substrate profiles of 10 Drosophila palmitoyl acyl transferases. Our results provide new insights and reveal many functional similarities of palmitoylation between Drosophila and humans.
date: 2022
type: Dissertation
type: info:eu-repo/semantics/doctoralThesis
type: NonPeerReviewed
format: application/pdf
identifier: https://archiv.ub.uni-heidelberg.de/volltextserverhttps://archiv.ub.uni-heidelberg.de/volltextserver/32549/1/Gonzalez_Sanchez_Juan_Carlos_PhD_Dissertation_06-12-22.pdf
identifier: DOI:10.11588/heidok.00032549
identifier: urn:nbn:de:bsz:16-heidok-325495
identifier:   Gonzalez Sanchez, Juan Carlos  (2022) Assessing functional impact of amino acid alterations in proteins.  [Dissertation]     
relation: https://archiv.ub.uni-heidelberg.de/volltextserver/32549/
rights: info:eu-repo/semantics/openAccess
rights: http://archiv.ub.uni-heidelberg.de/volltextserver/help/license_urhg.html
language: eng