Notes in Molecules and their Interaction

Interactions among Biomolecules

Short notes on interactions present within or between different biomolecules viz., protein, RNA, DNA and small molecule to analyze molecular docking and dynamics results.

Biomolecular Interactions

Biomolecular interactions play vital role in the performing biological functions and type of interaction determines the result and direction of the cascade. The article explores the methods and techniques used by present world researchers to decipher the talk between two biomolecules. This article has tried to cover both, in silico and in vitro aspects to let the reader grasp the usage of interterdesciplinary fields to decode the secrets of life.

Types of Interactions

Below are possible types of interactions to look for

  1. Protein-Protein
  2. Protein-Small Molecule (Ligand)
  3. Protein-DNA
  4. DNA-DNA
  5. DNA-RNA
  6. DNA-miRNA
  7. miRNA-miRNA
  8. RNA-RNA

In silico Study of Biomolecular Interaction

Different softwares and packages are there to study biomolecular interactions online. For better understanding the utilisation of packages can be divided as under

  1. Molecular Docking: AutoDock VINA, HEX, PatchDock, Haddock
  2. Molecular Dynamics: GROMACS, AMBER, NAMD, Desmond
  3. Analysis: Chimera, ChimeraX, PyMOL, VMD

How does these software work?

To use the packages of software, we might need to install them on local system, own server, explore access through remote server or they might be available as web services. They can be open-source or paid and few might be requiring high end computational setup.

Links for list of software packages

Molecular Docking: https://en.wikipedia.org/wiki/List_of_protein-ligand_docking_software

Molecular Dynamics: https://en.wikipedia.org/wiki/Comparison_of_software_for_molecular_mechanics_modeling

In vitro Study of Biomolecular Interaction

For in vitro study of Biomolecular Interactions, we need to understand few experiments. Following methods help in elucidating the biomolecular interactions:

  1. Spectroscopic Methods
  2. Surface Plasmon Resonance (SPR)
  3. Isothermal Titration Calorimetry
  4. Mass Spectrometry
  5. Nuclear Magnetic Resonance
  6. Enzyme-Linked Immunosorbent Assay

Spectroscopic Methods

 

Surface Plasmon Resonance

Isothermal Titration Calorimetry

 

Mass Spectrometry

 

Nuclear Magnetic Resonance

 

Enzyme-Linked Immunosorbent Assay