NATIONAL INSTITUTE OF TECHNOLOGY DURGAPUR

Course Name: Molecular Modelling and Drug Design

Course Code: BTE719
This presentation is solely meant for ACADEMIC PURPOSES and can be reused by others ONLY
for ACADEMIC USES with proper acknowledgments.
Reference Books:
1. Molecular Modelling And Drug Design By J.G. Vinter And Mark Gardner
2. Molecular Modelling: Principles And Applications By Andrew Leach
Some of the contents of the slides have been obtained from the following sites:
References:
1. http://www.nmr2.buffalo.edu/resources/edu/matr/nmr2_2004.pdf
2. https://www.ncbi.nlm.nih.gov/books/NBK22393/
3. https://users.cs.duke.edu/~brd/Teaching/Bio/asmb/Papers/Intro-reviews/flemming.pdf
4. https://www.slideshare.net/akashmahadev/cryo-electron-microscopy-124645726
5. https://www.youtube.com/watch?v=TVsiPcamK-0

Name of the Faculty: Dr. Amita Barik

Department Name: Biotechnology
Structure Determination Techniques

1. X-ray crystallography
2. Nuclear Magnetic Resonance (NMR)
3. Cryo-electron microscopy (Cryo-EM)

• Around 1,69,436 entries in the Protein Data Bank (PDB, Oct 2020),
• Of these, majority are determined by XRD (1,32,848 entries); NMR: 11473 entries

• So, one could say that the XRD method dominates the field of structural biology. The use of
protein structure information is currently widely spread within many areas of science and industry,
among which are biotechnology and pharmaceutical industry.
Structure Determination Techniques

• Primarily, the scientist has some kind of experimental data about the
structure of the molecule.

• For X-ray crystallography, this is the X-ray diffraction pattern.

• For NMR spectroscopy, it is information on the local conformation and

distance between atoms that are close to one another.
NMR Spectroscopy
• The protein is purified, placed in a strong magnetic field, and then probed with radio waves.
• The technique is currently limited to small or medium proteins, since large proteins present problems with
overlapping peaks in the NMR spectra.
• A major advantage of NMR spectroscopy is that it provides information on proteins in solution, as opposed to
those locked in a crystal or bound to a microscope grid, and thus, NMR spectroscopy is the premier method for
studying the atomic structures of flexible proteins.
• A typical NMR structure will include an ensemble of protein structures, all of which are consistent with the
observed list of experimental restraints.
• The structures in this ensemble will be very similar to each other in regions with strong restraints, and very different
in less constrained portions of the chain.
Why use NMR?

• Can’t get a crystal / want to work in solution

• Want to look at binding to other proteins/molecules
• Want to understand stability
• Want to measure fast dynamics processes
NMR vs X-ray crystallography

• In an x-ray diffraction pattern, each datum (reflection) contains information

about each atom in the asymmetric unit -each atom contributes information that
contributes to the intensity of each reflection
• In an NMR spectrum, each datum (peak) contains information about only a
single interatomic distance or angle -the process of determining a solution
structure by NMR is one of measuring many small distances and angles “one at a
time”
3D Electron Microscopy

• Electron microscopy, frequently referred to as 3D-EM, is also used to determine 3D

structures of large macromolecular assemblies.
• A beam of electrons and a system of electron lenses is used to image the biomolecule
directly.
• Several tricks are required to obtain a 3D structure from 2D projection images produced
by transmission electron microscopes.
• The most commonly used technique today involves imaging of many thousands of
different single particles preserved in a thin layer of non-crystalline ice (cryo-EM).
With so many structure determination
techniques available,

What is the need to predict protein

structure??
Computational Methods available for
structure prediction: