LS4201 : Structural Biology (Spring 2017) | Academic Portal of IISER Kolkata

Details of LS4201 (Spring 2017)

Level: 4

Type: Theory

Credits: 3.0

Course Code	Course Name	Instructor(s)
LS4201	Structural Biology	Partha Pratim Datta, Rituparna Sinha Roy

Syllabus
Peptide, proteins and Nucleic acids conformation: Organization of secondary structural elements of proteins; Structural motifs and analysis of informations from protein data bank; Origin and importance of Ramachandran Plot; Introductory structural bioinformatics; PHYSICAL INSTRUMENTS AND METHODS: Biomolecular structure determination using UV-Vis, IR, Electronic Circular Dichroism, Vibrational Dichroism, Dynamic Light Scattering, Fluorescence, Mass Spectroscopy and proteomics tools, Basic one dimensional and Two Dimensional NMR Spectroscopy and X-ray diffraction. Cryoelectron Microscopy: Basics of Scanning and Transmission Electron Microscopy, Sample preparation, single particle Cryo-Transmission Electron Microscopy, 3D Image processing from EM data, Molecular docking, Model building, computer simulation and graphics, Tomography;

Syllabus

Peptide, proteins and Nucleic acids conformation: Organization of secondary structural elements of proteins; Structural motifs and analysis of informations from
protein data bank; Origin and importance of Ramachandran Plot; Introductory structural bioinformatics;
PHYSICAL INSTRUMENTS AND METHODS:
Biomolecular structure determination using UV-Vis, IR, Electronic Circular Dichroism, Vibrational Dichroism, Dynamic Light Scattering, Fluorescence, Mass Spectroscopy and proteomics tools, Basic one dimensional and Two Dimensional NMR Spectroscopy and X-ray diffraction.
Cryoelectron Microscopy: Basics of Scanning and Transmission Electron Microscopy, Sample preparation, single particle Cryo-Transmission Electron Microscopy, 3D Image processing from EM data, Molecular docking, Model building, computer simulation and graphics, Tomography;

References
Ramachandran, G.N., and Sasisekharan, V. Advances in Protein Chemistry, Vol. 23, Academic Press, P. 283 (1968). Physical Biochemistry: Kensal E van Holde, Curtis Johnson, Pui Shing H Principles of Protein Structure: Schulz and Schirmer (1979) NMR of proteins and nucleic acids: K. Whtrich (1986). Molecular Biology of the Cell by Albert et al. (Electron microscopy) A passage through the ribosome by Cryo-EM, by Partha P. Datta and Ananya Chatterjee. Biophysical approaches to translational control of gene expression. Series: Biophysics for the Life Sciences, Vol. 1, Springer. SPIDER: http://www.wadsworth.org/spider\_doc/spider/docs/spider.html (Image processing) EMAN2: http://blake.bcm.edu/emanwiki/EMAN2 (Image processing) CHIMERA: http://www.cgl.ucsf.edu/chimera/ (Structure analysis) Additional reading: Three-Dimensional Electron Microscopy of Macromolecular Assemblies, by Joachim Frank, Oxford university press, 2006.

References

Ramachandran, G.N., and Sasisekharan, V. Advances in Protein Chemistry, Vol. 23, Academic Press, P. 283 (1968).
Physical Biochemistry: Kensal E van Holde, Curtis Johnson, Pui Shing H
Principles of Protein Structure: Schulz and Schirmer (1979)
NMR of proteins and nucleic acids: K. Whtrich (1986).
Molecular Biology of the Cell by Albert et al. (Electron microscopy)
A passage through the ribosome by Cryo-EM, by Partha P. Datta and Ananya Chatterjee. Biophysical approaches to translational control of gene expression. Series: Biophysics for the Life Sciences, Vol. 1, Springer.
SPIDER: http://www.wadsworth.org/spider\_doc/spider/docs/spider.html (Image processing)
EMAN2: http://blake.bcm.edu/emanwiki/EMAN2 (Image processing)
CHIMERA: http://www.cgl.ucsf.edu/chimera/ (Structure analysis)
Additional reading: Three-Dimensional Electron Microscopy of Macromolecular Assemblies, by Joachim Frank, Oxford university press, 2006.

Sl. No.	Programme	Semester No	Course Choice
1	IP	2	Not Allowed
2	IP	4	Core
3	IP	6	Not Allowed
4	MR	2	Not Allowed
5	MR	4	Not Allowed
6	MS	8	Core
7	RS	1	Elective
8	RS	2	Elective