Učni načrt predmeta

Vsebina:

Content (Syllabus outline):

Pri predmetu bomo proteinske strukture raziskovali z dveh zornih kotov: zakonov fizike in teorije evolucije. Z vidika fizike je nativna struktura proteina rezultat sil, ki delujejo na atome proteina in topila med procesom njegovega zvijanja, z biološke perspektive pa je nativna struktura proteina rezultat evolucije. Obe osnovni načeli sta tudi temelj metod, ki napovedujejo strukturo proteinov. Prvi način, de novo ali ab initio metode, poskuša napovedati strukturo proteinov le iz njihove sekvence, ne nanašajoč se na podobnost na nivoju zvitja med modelirano sekvenco proteina in znanimi strukturami. Drugi razred metod, ki vključuje primerjalno modeliranje, pa sloni na podobnosti večjega dela sekvence modeliranega proteina z vsaj eno že znano strukturo. Raziskovali bomo naravo sil, ki kontrolirajo nastanek določene proteinske strukture, nekatere vidike procesa zvijanja proteinov, primerjali proteinske sekvence, strukture proteinov, na vse načine modelirali proteine ter raziskovali strukturno genomiko in možnosti napovedi funkcije proteinov na osnovi predikcije njihove strukture.

Within this course, protein structures will be researched from two basic aspects: the laws of physics and the theory of evolution. From the aspect of physics, the native structure of proteins is the result of forces acting on the atoms of protein and solvent in the process of its folding, while from the biological aspect the native structure of protein is the result of evolution. Both basic principles also form the foundation for the protein structure prediction methods. The first, i.e., de novo or ab initio methods attempt to predict the structure of proteins from their sequence alone, not referring to the similarity at the level of folding between the modelled protein sequence and known structures. The second class of methods, which includes comparative modelling, is based on the similarity between the major part of the sequence of modelled protein and at least one known structure. We will research the nature of forces controlling the formation of a particular protein structure and certain aspects of the protein folding process, compare protein sequences, and protein structures, model proteins in many different ways, and research structural genomics and the possibilities for predicting the functions of proteins by predicting their structure.