Molecular Biology Refresher Course - Research … Reverse Transcription Translation Epigenetics post-translational modifications POST-TRANSLATIONAL MODIFICATIONS Essential for proper

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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