Caricamento in corso...
Structural models for the investigation of protein dynamics
01DMARW
A.A. 2021/22
Course Language
Inglese
Degree programme(s)
Doctorate Research in Ingegneria Civile E Ambientale - Torino
Course structure
| Teaching | Hours |
|---|---|
| Lezioni | 15 |
Lecturers
| Teacher | Status | SSD | h.Les | h.Ex | h.Lab | h.Tut | Years teaching |
|---|---|---|---|---|---|---|---|
| Lacidogna Giuseppe | Professore Associato | CEAR-06/A | 4,5 | 0 | 0 | 0 | 1 |
Co-lectures
Context
| SSD | CFU | Activities | Area context | *** N/A *** |
|---|
Questo corso ha l’obiettivo di analizzare la dinamica delle proteine da un punto di vista numerico e sperimentale. Inizialmente, verranno presentate due delle principali tecniche spettroscopiche (Raman e THz- TDS) utilizzate per l’analisi delle vibrazioni a bassa frequenza delle proteine. In seguito, gli approcci e le metodologie di calcolo utilizzate nella letteratura per lo studio della dinamica delle proteine verranno ampiamente descritti, con particolare attenzione ai modelli basati sull’analisi modale (NMA) e modelli reticolari elastici (ENMs). La stretta correlazione tra le vibrazioni a bassa frequenza delle proteine ed il loro meccanismo e funzione biologica verrà ampiamente analizzato. Infine, si faranno anche cenni relativi allo studio numerico della flessibilità e ai cambi conformazionali delle proteine ottenuti tramite l’applicazione di forze su modelli reticolari elastici.
This course aims at exploring the realm of protein dynamics from a numerical and experimental point of view. First, spectroscopy techniques, such as Raman and THz-TDS, will be presented with special focus on the detection and analysis of low-frequency protein vibrations. Afterwards, the numerical approaches adopted in the literature for the understanding of protein dynamics will be surveyed, with special attention to Normal Mode Analysis (NMA) and coarse-grained elastic network models (ENMs). The strict relationship between low- frequency protein vibrations and the protein biological mechanism and functionality will be also investigated. Final remarks will be also given regarding the numerical investigation of protein flexibility by means of force application.
Nessuno
None
Il corso si compone di 10 lezioni da 1.5 ore, per una durata complessiva di 15 ore, così organizzate:
(1) “Introduction to the course: wave and vibrational phenomena at different scales. Proteins: structure and
function”.
(2) “Raman spectroscopy: fundamentals and applications to proteins”.
(3) “THz-TDS: fundamentals and applications to proteins”.
(4) “Protein dynamics: from Molecular Dynamics to Normal Mode Analysis (NMA) of elastic models”
(5) “Coarse-grained elastic network models (ENMs) for protein dynamics: GNM and ANM”
(6) “Structural Mechanics-based elastic lattice models (ELMs) for protein dynamics”
(7) “Protein conformational changes and their correlation with the normal modes of vibrations”
(8) “New coarse-grained elastic models to predict large-scale protein conformational changes: NOLB and
hdANM”
(9) “Application of static forces of protein structures to probe flexibility and conformational changes”
(10)“Putting together force application and dynamics: applying dynamic forces drives protein conformational
changes”
The course is made up of 10 lesson 1.5 hour-long, for a total duration of 15 hours. The schedule is as follows:
(1) “Introduction to the course: wave and vibrational phenomena at different scales. Proteins: structure and
function”.
(2) “Raman spectroscopy: fundamentals and applications to proteins”.
(3) “THz-TDS: fundamentals and applications to proteins”.
(4) “Protein dynamics: from Molecular Dynamics to Normal Mode Analysis (NMA) of elastic models”
(5) “Coarse-grained elastic network models (ENMs) for protein dynamics: GNM and ANM”
(6) “Structural Mechanics-based elastic lattice models (ELMs) for protein dynamics”
(7) “Protein conformational changes and their correlation with the normal modes of vibrations”
(8) “New coarse-grained elastic models to predict large-scale protein conformational changes: NOLB and
hdANM”
(9) “Application of static forces of protein structures to probe flexibility and conformational changes”
(10)“Putting together force application and dynamics: applying dynamic forces drives protein conformational
changes”
A distanza in modalità sincrona
On line synchronous mode
Presentazione orale
Oral presentation
P.D.2-2 - Aprile
P.D.2-2 - April