Learning objectives
At the end of the course, the student should have learnt and understood the main features of protein structures and the fundamental physical and biological principles that underlie the methodologies and techniques explained. In particular, the student must be able to:
1. consult the main biological databanks, particularly of protein sequences and structures
2. starting from a protein sequence, obtain all the available structural/functional informations
3. analyze the structural features of a protein by means of molecular graphics softwares
4. built a structural model of a protein of known sequence
5. run a molecular dynamics simulation of a protein system
6. run a molecular docking simulation of a protein system
7. relate all the useful data to understand the fundamental properties of the system under study, in particular regarding the structure-activity relationship
8. use the specific terminology
9. consult and understand the scientific literature
In addition, the student should be able to choose the better approach for the study of a specific problem regarding a protein system, and to verify its efficacy and usefulness, searching solutions by themselves and developing their knowledge in depth.
Finally, the student should be able to communicate the results of their analyses and studies in a clear, complete and incisive manner. Such ability will be exerted particularly during the course, in which the drawing up of a written report of each practice performed in the lab will be required.
Prerequisites
None.
Course unit content
Protein structure. Covalent and not-covalent interactions that are present in a biomolecular structure. Theoretical and experimental methods for determining secondary and tertiary protein structure. Topological representation. Supersecondary structures. Ramachandran plot. Fold classification.
Search engines in biological databases.
Protein and nucleic acid sequence analysis: similarity and sequence alignment tools (pairwise and multiple). Patterns and conserved motifs recognition. Protein physico-chemical profiles. Secondary structure prediction from the protein sequence.
Analysis of structural and functional features of proteins and protein complexes by means of molecular graphics softwares and web servers.
Computational techniques for the study of protein structure and dynamics:
Molecular mechanics and force fields; energy minimization; molecular dynamics simulations.
Molecular recognition. Molecular interaction simulations: docking and drug design.
Practices in the lab during the course.
Full programme
Protein structure. Covalent and not-covalent interactions that are present in a biomolecular structure. Theoretical and experimental methods for determining secondary and tertiary protein structure. Topological representation. Supersecondary structures. Ramachandran plot. Fold classification.
Search engines in biological databases.
Protein and nucleic acid sequence analysis: similarity and sequence alignment tools (pairwise and multiple). Patterns and conserved motifs recognition. Protein physico-chemical profiles. Secondary structure prediction from the protein sequence.
Analysis of structural and functional features of proteins and protein complexes by means of molecular graphics softwares and web servers.
Computational techniques for the study of protein structure and dynamics:
Comparative modeling and fold recognition methods.
Molecular mechanics and force fields; energy minimization; molecular dynamics simulations.
Molecular recognition. Molecular interaction simulations: docking and drug design.
Practices in the lab during the course.
Bibliography
A.M. Lesk, "Introduction to protein science", Oxford Univeristy Press.
A.M. Lesk, "Introduzione alla Bioinformatica", McGraw-Hill Ed.
G. Valle, M. Helmer Citterich, M. Attimonelli, G. Pesole, "Introduzione alla Bioinformatica", Zanichelli Ed.
D.E. Krane, M.L. Raymer, "Fondamenti di Bioinformatica", Pearson Education Ed.
The slides used for the lessons and some review articles will be given.
Teaching methods
Oral lessons and practices in the laboratory.
For the oral lessons the teacher will use some slides that will be part of the educational material. These slides will be uploaded on the "Elly" platform some days before the beginning of each new argument. In addition, some review articles will be given. To download the educational material, the on-line registration to the course is needed.
For each topic explained, there is a practical exercise in the lab, performed by means of a computer and, in some cases, of the high performance computing cluster of our department. During the practical exercises, both databanks and web server, and several software for analyses and calculations will be used. The practical exercises first will be led by the teacher on an example system, then will be performed personally by the student, to provide them with advanced techniques and methodologies in the field of computational biophysics, in particular for the determination, prediction and analysis of the structure and the dynamics of protein systems.
A written report of each practice performed in the lab will be required, in which the student will explain the studied system, the methods used, the results obtained, the conclusions and the comments. Such reports could be given during the course (and in such a case, checked by the teacher); in any case, the reports will be due a couple of days before the exam, and will be corrected and evaluated. Therefore, the delivering of the reports is needed to do the exam.
Students have to check on the "Elly" platform the availability of the educational material and the notices from the teacher.
Assessment methods and criteria
Oral exam. As reported above, a written report of each practice performed in the lab will be required, in which the student will explain the studied system, the methods used, the results obtained, the conclusions and the comments. Such reports could be given during the course (and in such a case, checked by the teacher); in any case, the reports will be due a couple of days before the exam, and will be corrected and evaluated. Therefore, the delivering of the reports is needed to do the exam. The exam will start from the discussion of the reports; some questions on the fundamental concepts of the studied techniques will follow. These two parts have the same weight on the final evaluation.
Other information
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