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
- Protein-Protein
- Protein-Small Molecule (Ligand)
- Protein-DNA
- DNA-DNA
- DNA-RNA
- DNA-miRNA
- miRNA-miRNA
- 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
- Molecular Docking: AutoDock VINA, HEX, PatchDock, Haddock
- Molecular Dynamics: GROMACS, AMBER, NAMD, Desmond
- 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:
- Spectroscopic Methods
- Surface Plasmon Resonance (SPR)
- Isothermal Titration Calorimetry
- Mass Spectrometry
- Nuclear Magnetic Resonance
- Enzyme-Linked Immunosorbent Assay
Spectroscopic Methods
Surface Plasmon Resonance
Isothermal Titration Calorimetry
Mass Spectrometry
Nuclear Magnetic Resonance
Enzyme-Linked Immunosorbent Assay