Protein computational analysis
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This document discusses the computational study of protein structure and function from sequence. It begins by defining proteins as polypeptides made of amino acids that fold into 3D structures like helices and sheets. The document then outlines the steps to computationally analyze a protein, including obtaining the sequence from databases in FASTA format, predicting properties with tools like ProtParam, secondary structure with PsiPred, signal peptides with SignalP, transmembrane regions with TMHMM, and domains with InterPro. It describes using homology-based tools to leverage structural conservation and then discusses challenges in full 3D structure prediction. The overall summary describes the computational workflow to go from a protein's amino acid sequence to analyzing its structure and function.
Protein computational analysis
- 1. Computational study of Protein From Scratch; From Structure to Function Topic: Kinza Irshad Soil and Ecosystem Ecology Lab, COMSATS University Islamabad, Abbottabad 5/28/2019 1
- 2. What is Protein? Long chain polypeptides Made up of 20 naturally occurring amino acids Two amino acids have peptide bond, having double bond characteristic Functional proteins are folded into 3D structure, containing helix, Beta sheets and loops Helix and sheets are rigid part while loops are flexible In 3D structure hydrophobic amino acids are located in core while hydrophilic are oriented at surface. 5/28/2019 2
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- 4. Folding State of Protein 5/28/2019 4
- 5. First Step; Protein Sequence We are going to take start from Protein Sequence. We can take protein sequence from database or can translate gene sequence into protein. In both cases, we should ultimately have FASTA format. 5/28/2019 5
- 6. What is FASTA Format??? >MH08765.1 Serine_protease, Human ELPDFTPLVEQASPAVVNISTRQKLPDRAMARGQLSIPDLEGLPPMFRDFLERSIPQVPRNPRGQQREAQSLGSGFIISN DGYITNNHVVADADEILVRLSDRSEHKAKLIGADPRSDVAVLKIEAKNLPTLKLGDSNKLKVGEWVLAIGSPFGFDHSVTA GIVSAKGRSLPNESYVPFIQTDVAINPGNSGGPLLNLQGEVVGINSQIFTRSGGFMGLSFAIPIDVALNVADQLKKAGKVS RGWLGVVIQEVNKDLAESFGLDKPSGALVAQLVEDGPAAKGGLQVGDVILSLNGQSINESADLPHLVGNMKPGDKINL DVIRNGQRKSLSMAVGSLPDDDEEIASMGAPGAERSSNRLGVTVADLTAEQRKSLDIQGGVVIKEVQDGPAAVIGLRPG DVITHLDNKAVTSTKVFADVAKALPKNRSVSMRVLRQGRASFITFKLA 5/28/2019 6 Header Region Protein Sequence in one letter code
- 7. How To Get Protein Sequence from Database?? 1. We are going to take example of largest and most frequently used NCBI nucleotide and Protein database https://www.ncbi.nlm.nih.gov/ 2. There are two different types of format ◦ GenBank ◦ FASTA 5/28/2019 7
- 8. After Having Sequence What to Do? In next step, We will try to figure out Physio-chemical properties of our target protein, including Molecular weight, Iso-electric point, stability, etc. We will use very popular tool here, named Expasy Protparam. https://web.expasy.org/protparam/ The input is protein sequence in FASTA format. Genbank format is not acceptable 5/28/2019 8
- 9. Prediction of Secondary Structure Elements There are three different structural forms of proteins, primary, secondary, and tertiary structure. In secondary structure, there will be three different type of element, alpha-helix, beta-sheets and loops. Two different type of algorithms used to predict secondary structure elements I. Ab-initio Based II. Homology Based 5/28/2019 9
- 10. Prediction of Secondary Structure Elements Ab-initio algorithms are stand alone algorithms, identifying the secondary structure elements of using intrinsic tendencies of amino acids to be in particular confirmation. For example, glycine and proline, they love to stay in loops only Homology-based algorithms make prediction based on secondary structure of homolgous. Structures are more conserved as compared to sequence. 5/28/2019 10
- 11. PSI-PRED; A Homology-Based Tool We will use Psi-Pred a homology based tool to predict secondary structure http://bioinf.cs.ucl.ac.uk/psipred/ The submitted protein sequence will be searched in protein database through BLAST to search the homologous sequences, based on query coverage and E-value. The tool will align the homologous sequences (MSA) to get information about conservancy. The conserved regions should ideally have same secondary structural elements. 5/28/2019 11
- 13. Signal Peptide Prediction Signal peptide in defining localization of protein in the cells. Present at N-terminal of newly synthesized protein Predominantly hydrophobic amino acids Important to predict especially if we want to clone the gene into expression system. 5/28/2019 13
- 14. Signal Peptide Prediction Commonly used algorithm for the prediction of signal peptide is SignalP4.1 http://www.cbs.dtu.dk/services/SignalP/ Input sequence is FASTA format 5/28/2019 14
- 15. Is Our Protein is Transmembrane ? In cell, proteins are either globular or transmembrane. Transmembrane proteins can be i. Transmembrane helical ii. Beta-barrels To make structural prediction of transmembrane protein TMHMM (Transmembrane Hidden Markov Model) algorithm is used. http://www.cbs.dtu.dk/services/TMHMM/ 5/28/2019 15
- 16. Prediction of Domains & Motifs in Protein Structure InterPro online server will be used to identify the domains https://www.ebi.ac.uk/interpro/ The input sequence will be in FASTA format. InterPro used homology search to identify the domains and mortifies. 5/28/2019 16
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- 18. 3D Structure predication of a protein Protein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence—that is, the prediction of its folding and its secondary and tertiary structure from its primary structure. Structure prediction is fundamentally different from the inverse problem of protein design. Protein structure prediction is one of the most important goals pursued by bioinformatics and theoretical chemistry; it is highly important in medicine (for example, in drug design) and biotechnology (for example, in the design of novel enzymes).
- 19. 3D Structure Prediction of Protein 3D structure prediction is one of most complicated computational process Important step for protein structure analysis There are three experimental techniques to determine 3D structure of proteins i. X-ray Crystallography ii. NMR iii. Cryo-Electron Microscopy 5/28/2019 DEPARTMENT OF BIOCHEMISTRY & BIOTECHNOLOGY 19
- 20. Structure prediction of a protein
- 21. 5/28/2019 21 End of Session No 1 Lets do some practical work Accession # MH045598 https://www.ncbi.nlm.nih.gov/ https://web.expasy.org/protparam/ http://bioinf.cs.ucl.ac.uk/psipred/ http://www.cbs.dtu.dk/services/SignalP/ https://www.ebi.ac.uk/interpro/ https://zhanglab.ccmb.med.umich.edu/I-TASSER/
- 22. 5/28/2019 22 Thank You & Happy to Answer The Questions