Thank you for joining us on the Bio-protocol Ambassador Roundtable webinar on Protein Protein Interaction Techniques.
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⏰ Timestamps
0:00 Introduction
01:00 About the Speaker, Dr Shayon Bhattacharya
02:38 Overview of Protein-Protein Interactions, PPIs
05:00 Different types of PPI based on composition, lifetime, affinity
07:05 Predicting PPIs using in silico modelling methods: Sequence-based, structure-based and Physics-based approaches
08:52 Introduction to Molecular Dynamics (MD) Simulation
09:52 Typical workflow of MD simulation
12:17 Step-by-step breakdown of MD simulation workflow
14:33 Molecular mechanics force fields
16:54 Explicit water models
18:50 About commonly used force fields and water models
20:25 PPIs in peptide self-assembly: finding drug targets for neurodegenerative diseases and its challenges
26:45 Optimising short-range intra-protein interactions in Alzheimer's and Parkinson's
28:05 Targeting long-range intra-protein interactions
31:06 Optimising the monomer-monomer PPI in the design of alpha-Synuclein tetramer
32:53 Why are alpha-Synuclein tetramers more ubiquitous than other helical oligomers?
35:10 Further research insights on drug designing for Alzheimer's and Parkinson's
42:40 About the Speaker, Dr Vinay Kumar ldikuda
43:44 Overview of single-molecule approaches to study protein-ligand interactions
44:59 About Hyperpolarization-activated cyclic nucleotide-gated, HCN channel
46:16 Measurement of cAMP in HCN channels: bulk vs single-molecule
48:12 TIRF microscopy to decrease the excitation volume; upto10 nM ligand concentration
50:00 Measurement in micromolar/millimolar physiological range: Zero mode waveguides, ZMW
53:00 Workflow for studying PPI using ZMW
54:45 Statistical modeling of single-molecule trajectories and data representation
56:49 ZMW for PPI studies
58:40 Summary and conclusion
QnA
1:00:35 Can ZMW be used for studying transient PPIs?
1:00:58 How long does it take to develop a functional assay for a new interaction?
1:01:28 How to quantify of labelling efficiency?
1:03:05 About the Speaker, Dr Hanna Kratzat
1:04:50 History of NanoTemper
1:06:10 Characterizing interactions with different types of molecules/samples and its challenges
1:09:53 Principles of MicroScale Thermophoresis (MST)
1:12:45 How does an MST experiment data look like?
1:14:18 Applications of MST (examples)
1:15:45 Analyzing binding of misfolding-prone antibody to chaperone protein
1:19:50 pH-dependent binding affinity changes in proteins
1:21:55 Study of membrane fluidity using nanodisc
1:23:55 Detection of interactions at isothermal conditions with spectral shift and some examples of its application
1:27:18 Consumables for Monolith instrument and overview of its application
QnA
1:30:40 Limitation of type of samples to be analysed with this method-instrument
1:31:52 Is it possible to study lipid binding to proteins with this technology?
1:33:05 What are the advantages of MST over SPR or ITC?
1:34:55 Concluding remarks
🥼About Bio-protocol Ambassador Roundtable:
Bio-protocol is an online peer-reviewed protocol journal curating and hosting high-quality, open-access, step-by-step protocols across the life sciences. Our motto is to improve research reproducibility and through our ambassador roundtable webinar program for young researchers, we aim to openly discuss protocols, ideas and cutting-edge life science technologies.
~This webinar recording is on protein-protein interactions
#protein #interaction #biochemistry
Speakers:
Dr Shayon Bhattacharya, Senior Postdoctoral Researcher, University of Limerick
Dr Vinay Kumar ldikuda, Postdoctoral Fellow, Washington University
Dr Hanna Kratzat, Field Application Specialist, NanoTemper Technologies
Organizers:
Meet the Bio-protocol Ambassadors at https://bio-protocol.org/en/ambassado...
Mariella Quispe-Carbajal, PhD candidate, Stony Brook University
John Downey, PhD candidate, EPSRC-SFI Centre
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