molecular biology refresher course - research … reverse transcription translation epigenetics...
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Molecular Biology Refresher Course28 Oct 2016
Protein Modifications Introduction to databases, protein-protein Interaction networks
and visualization tools
Instructor:
Dr. Sumit Saurabh email –[email protected]
Post doctoral Associate Alt ID – [email protected]
Baylor College Of MedicineNeurological Research Institute
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• Introduction
• Protein Modification Databases
• Protein Visualization Tools
• Protein-Protein Networks
OUTLINE
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DNA
RNA
Protein
Replication
Transcription Reverse Transcription
Translation
Epigenetics
post-translational modifications
POST-TRANSLATIONAL MODIFICATIONSEssential for proper functioning and diversifies functional repertoire
Mature Protein Product3
Cellular sites associated with protein synthesis
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Basic concepts about PTMs
•PTMs are chemical modifications of residues on a
protein during or after its translation.
•PTMs regulates protein properties, such as folding,
activity, localization, stability, degradation and
interacting partners.
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Types of Modification6
Targeting protein lipidation in disease (Review)
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Epigenetic modifications and human disease
Nature Biotechnology
(2010)
doi:10.1038/nbt.1685
Example10
Rsk-2 activity is necessary for epidermal growth factor-induced phosphorylation of CREB protein and
transcription of c-fos gene. PNAS 1998 (RPS6KA3 modifies Histone H3)
(a–d) Facial views of a boy with CLS at different ages showing evolution during infancy of facial gestalt. (a)At 9 months, (b) at 18 months, (c) at 3 years, and (d) at 6 years. Note the large forehead, hypertelorism, downslantingpalpebral fissures, long philtrum, anteverted nares, and thick lips. This boy carries an RPS6KA3 intragenic duplication previously reported.(e–g) Views of the hands of the same patient. Note the typical broad tapering fingers (e) at 9 months, (f) at 18 months, and (g) at 5 years.
Coffin–Lowry syndrome (CLS; OMIM 303600)
Highly heterogeneous loss-of-function mutations in
the RPS6KA3 gene are responsible for CLS.
European Journal of Human Genetics (2010) 18, 627–633; doi:10.1038/ejhg.2009.189
Example11
Handbook of Clinical Neurology
Volume 113, 2013, Pages 1737–1743
Pediatric Neurology Part III
Chapter 179 – Congenital disorders of glycosylation
More examples and references12
Mechanisms that regulate GPCR desensitization and internalization
Phosphorylation
Nature Reviews Drug Discovery 11, 69-86 (January 2012)
Example13
Phosphorylation sites are underlined.
Phosphorylation Motifs of Common Kinases
Helps in Prediction14
Building ubiquitin chains: E2 enzymes at workNature Reviews Molecular Cell Biology, November 2009
Ubiquitination and protein degradation
Ubiquitin
Example15
1. Post Translational Modification Databases
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Exercise17
Exercise
CLICK Categories>Post translational modification>NetPhos
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Src Family Kinases
Int J Biol Sci 2012; 8(10):1385-1397. doi:10.7150/ijbs.514119
>NP_114183.1 proto-oncogene tyrosine-protein kinase Src [Rattus norvegicus] MGSNKSKPKDASQRRRSLEPAENVHGAGGAFPASQTPSKPASADGHRGPNAAFVPPAAAEPKLFGGFNSS DTVTSPQRAGPLAGGVTTFVALYDYESRTETDLSFKKGERLQIVNNTRKVDVREGDWWLAHSLSTGQTGY IPSNYVAPSDSIQAEEWYFGKITRRESERLLLNAENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKH YKIRKLDSGGFYITSRTQFNSLQQLVAYYSKHADGLCHRLTTVCPTSKPQTQGLAKDAWEIPRESLRLEV KLGQGCFGEVWMGTWNGTTRVAIKTLKPGTMSPEAFLQEAQVMKKLRHEKLVQLYAVVSEEPIYIVTEYM NKGSLLDFLKGETGKYLRLPQLVDMSAQIASGMAYVERMNYVHRDLRAANILVGENLVCKVADFGLARLI EDNEYTARQGAKFPIKWTAPEAALYGRFTIKSDVWSFGILLTELTTKGRVPYPGMVNREVLDQVERGYRM PCPPECPESLHDLMCQCWRKEPEERPTFEYLQAFLEDYFTSTEPQYQPGENL
proto-oncogene tyrosine-protein kinase Src [Rattus norvegicus]
NCBI
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Exercise
NP_114183.1 proto-oncogene tyrosine-protein kinase Src[Rattus norvegicus] Refer to NCBI – Type the accession no
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http://phospho.elm.eu.org/pELMBlastSearch.html
Phospho.ELM: A database of experimentally verified
phosphorylation sites in eukaryotic proteins
Exercise23
One more Database!24
2. Protein visualization tools and resources
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Structural
information
about protein
of interest
Download PDB
files to
visualize in
CHIMERA
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PDB GSK3 (PDB-ID 5K5N)
Homology Models help
in predicting sites of Modification
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UCSF CHIMERA
CHIMERA – Protein Visualization Tool
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Example – GSK3β Chain A
STRUCTURE and SEQUENCE OF GSK3β rendered in CHIMERA
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http://string-db.org/
Protein-Protein Interaction Networks
To find interactions and establish
pathways, important hubs and nodes
involved in diseases
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http://string-db.org/
Protein-Protein Interaction Networks
To find interactions and establish
pathways, important hubs and nodes
involved in diseases
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ANKRD11
BCKDK
BCL11A
CACNA1H
CACNA2D3
CHD2
CNTN4
CNTNAP2
CTNND2
CUL3
DEAF1
DSCAM
ERBB2IP
FOXP1
GABRB3
GRIP1
ILF2
INTS6
IRF2BPL
KAT2B
KATNAL2
KDM5B
KMT2A
KMT2C
MAGEL2
MED13L
MET
MSNP1AS
MYT1L
NLGN3
NRXN1
PTCHD1
RANBP17
RELN
SHANK2
SLC6A1
SPAST
USP7
WAC
Strong Candidate Genes from SAFARI gene listNetwork Representation
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ANKRD11
BCKDK
BCL11A
CACNA1H
CACNA2D3
CHD2
CNTN4
CNTNAP2
CTNND2
CUL3
DEAF1
DSCAM
ERBB2IP
FOXP1
GABRB3
GRIP1
ILF2
INTS6
IRF2BPL
KAT2B
KATNAL2
KDM5B
KMT2A
KMT2C
MAGEL2
MED13L
MET
MSNP1AS
MYT1L
NLGN3
NRXN1
PTCHD1
RANBP17
RELN
SHANK2
SLC6A1
SPAST
USP7
WAC
Strong Candidate Genes from SAFARI gene listNetwork Representation
Genes implicated in nervous system development
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Instructor:
Dr. Sumit Saurabh
Post-Doctoral Associate Email - [email protected]
Baylor College Of Medicine
Neurological Research Institute
Thank you!
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