Laboratory of Biomolecular Modeling and Dynamics
Institute for Protein Research

Independent Associate Professor

Sandhya P. Tiwari

sandhyatiwari

URL: http://www.protein.osaka-u.ac.jp/modellingdynamics/sandhyaptiwari

Unlocking the Intricacies of Protein Structures:
A Journey into Biologically Relevant Dynamics
through Computational Modeling andSimulations
Proteins, the building blocks of life, are not staticentities; they possess a dynamic nature, akin toany other object on Earth. At our laboratory, wedelve into the fascinating world of proteins,
employing structural data gleaned from advanced
experimental techniques like X-ray
Crystallography, cryo-electron microscopy, andsmall-angle X-ray scattering. Our mission? To
model the myriad conformations these proteinscan adopt in solution and, employing theprinciples of physics, simulate their flexible
movements — their dynamics — deciphering thevery essence of their functioning.

3) **Integrating Insights:** Manyexperimental methods provide dynamic
glimpses but lack molecular resolution. We
develop methods that amalgamate informationfrom diverse sources, building a reliable
understanding of the system under scrutiny.

Our research spans a wide spectrum ofintriguing topics:- **Protein Allostery:** Unraveling themysteries of protein regulation.
- **Oligomerization and BiologicalComplex Assembly:** Investigating theintricate dance of protein interactions.
- **Evolutionary Conservation ofStructure and Dynamics:** Exploring theancient echoes within protein architectures.
- **Proteins of Interest:** Delving deep
into proteins like TIM Barrel fold proteins,PyrR, dihydrofolate reductase, leukotrienealpha-4 hydrolase, and more.

Our arsenal of methods includes, but is notconfined to:- **Python Programming:** Harnessing thepower of coding for intricate analyses.
- **Statistical Analysis:** Extracting
meaningful insights from complex datasets.
- **Bioinformatics Tools:** Employing
advanced tools for sequence alignment andstructure prediction.
- **Molecular Dynamics Simulations:**
Simulating the dynamic dance of proteins at themolecular level.
- **Normal Mode Analysis:** Probing thefundamental modes of protein motion.
- **Deep Learning Approaches:** Leveraging
the potential of artificial intelligence fornuanced understanding.
- **Biomolecular Visualization andAnimation:** Crafting visual narratives that
illuminate the intricate world of proteins.
- **Web-Based Tool Development:** Creatinguser-friendly interfaces for the broader
scientific community.

Our approach is multifaceted, addressing theunique challenges posed by protein structures:
1) **Completing the Puzzle:** Protein
structures often present with missing
information, requiring us to analyze analogous
structures to fill the gaps.
2) **Taming the Data Deluge:** Copious
amounts of data can overwhelm, necessitating
innovative strategies. We employ techniquessuch as simplifying their representationthrough coarse-graining and utilizing methods
like elastic network model-based normal mode
analysis, which do not demand exhaustive
details of their motions.

Join us on this expedition, wherewe unravel the enigmatic world ofproteins, one dynamic movement
at a time.

Institute for Protein Research, Osaka University
3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
TEL: +81-6-6879-4332
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