Homology modelling and generation of 3D-structure of protein (G).pptx

Homology modeling, also known as comparative modeling, is a computational method used to predict the three-dimensional (3D) structure of a protein based on its amino acid sequence. This technique relies on the principle that proteins with similar amino acid.

1. Homology modelling and generation of 3D-structure of protein Presented by – Garima Singh Masters of Pharmacy 1 st year (2 nd semester) School of Pharmaceutical Sciences {Pharmaceutical Chemistry} COMPUTER AIDED DRUG DESIGN

2. Contents Introduction Protein 3D structure generation Homology Modeling History Homology Modeling steps Advantages & Disadvantages References

3. Protein 3 D structure generation Protein 3D structures are obtained using two popular techniques, x-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy. There are many protein for which the sequence information is available , but their three-dimensional structures remain unknown. Therefore, it is often necessary to obtain approximate protein structures through computer modelling. There are three computational approaches to protein 3D structural modelling and prediction. They are Homology modelling, threading, and ab initio prediction. 1

4. Homology modeling Homology modelling , also known as comparative modelling , is a method used to predict the 3D structure of a protein with an unknown structure by using the known structure of a homologous protein from : It’s amino acid sequence and An experimental 3D structure of a related homologous protein ( the “template”). The method relies on the fact that the 3D structure of proteins is often better conserved than their amino acid sequence. Therefore, proteins with similar sequences are likely to have similar structures. 2

5. If similarity between the target sequence and the template sequence us detected , structural similarity can be used. In general, 30% sequence identity is required to generate an useful model. An Example – To know the structure of sequence A ( 150 amino acids long ), 1 st of all compare sequence A to all the sequences of known structures stored in the protein data bank (using, for e.g. BLAST), if a sequence B ( 300 amino acids long ) containing a region of 150 amino acids that match sequence A with 50% identical residues. As this match (alignment) clearly falls in the safe zone ( 50% ), we can simply take the known structure of sequence B ( the template ), cut out the fragment corresponding to the aligned region, mutate those amino acids that differ between sequences A and B , and finally arrive at our model for Structure A . Structure A is called the target and is of course not known at the time of modeling. 3

6. History The first homology modelling studies were done using wire and plastic models of bonds and atoms. As early as 1960’s the models were constructed by taking the coordinates of a known protein structure and modified by hand for those amino acids that did not match the structure. In 1969 David Phillips, Brown and co-workers published the first paper regarding homology modelling. They modelled α -lactalbumin based on the structure of hen-egg white lysozyme. The sequence identify between these two proteins was 39%. 4

7. Homology modelling steps Template recognition and initial alignment Alignment of the query sequence with the template Building a 3D model of the Query protein Loop modelling Side-chain modelling Model optimization Model validation and Evaluation 5

8. 1.) Template recognition and initial alignment Identifying and selecting appropriate template structures from the Protein Data Bank (PDB). To identify appropriate templates , pair-wise sequence alignment methods such as BLAST can be used to identify proteins with high sequence homology to the query protein. Once several templates are identified , most appropriate ones are chosen for modelling. 2.) Alignment of the Query sequence with the Template It is essential to achieve a high-quality Sequence alignment as it directly impacts the accuracy of the resulting model. A homology model can only be as good as the sequence alignment. 6

9. Multiple sequence alignment is preferred as it contains evoluti onary information that is important for structure and function. Effective multiple sequence alignment programs like Proline and T-Coffee are recommended for use. 3.)Building a Three-Dimensional model of the Query Protein There are different methods used for generating 3D models of proteins based on its template. Classified into 4 categories : Rigid-body assembly- the rigid body parts are picked up from the template protein structures and brought together using tools like BUILDER , and SWISS MODEL. Segment matching- involves using a cluster of atomic positions, which are used to select segments . These segments are aligned with the template structure to create a model of target protein , can be done with SEGMOD/ENCAD. 7

10. C. Spatial restraint method – it builds protein structures by applying spatial restraints to guide the building of a model that closely matches the template structure. MODELLER is a software package commonly used to perform this method . d. Artificial evolution method- involves using the rigid-body assembly method and stepwise template evolutionary mutations together until the template sequence is the same as the target sequence, can be performed with NEST. 4.) Loop Modelling There are often gaps or insertions that can be occur in sequence alignments when modelling proteins , which are called loops and are structurally less conserved during evolution. There are 2 main methods for loop prediction – Database search method Conformational search method Specialised programs for loop modelling – FREAD , PETRA , and CODA . 8

11. 5.) Side chain modelling A process of predicting the conformation of the side chains of amino acids in a protein structure, crucial in evaluating protein-ligand and protein-protein interactions. Searching every possible conformation of a side chain is computationally time-consuming and no effective so, most side chain prediction programs use the preferred conformation called Rotamers. Various tools for side chain modelling – RAMP and SCWRL . 6.) Model optimization Model optimization refers to the process of refining the initial model to improve its accuracy and reliability. This optimization process involves adjusting the positions of the atoms in the model to reduce any clashes or steric hindrances between atoms. 9

12. 7.) Model validation and Evaluation After building the 3D model of the query protein , it is essential to validate and evaluate its quality to ensure that it is biologically relevant and can be used for further studies . It involves comparing the model to real experimental 3D structures and using various evaluation methods to assess the model’s stereochemistry , physical parameters , knowledge-based parameters , statistical mechanics , and other criteria. Some commonly used programs are – WHATIF , PROCHECK and PROSA. 10

13. Advantages Disadvantages It can find the location of alpha carbons inside the folded protein. It can help to guide the mutagenesis experiments , or hypothesize structure-function relationship. The position of conserved regions of the protein surface can help identify putative active sites , binding pockets and ligands. Homology models are unable to predict conformations of insertions or deletions, or side chain positions with a high level of accuracy. Homology models are not useful in modeling and ligand docking studies necessary for the drug designing and development process. 11

14. References Vyas, V. K., Ukawala , R. D., Ghate , M., & Chintha , C. (2012). Homology Modeling a Fast Tool for Drug Discovery: Current Perspectives. Indian Journal of Pharmaceutical Sciences, 74(1), 1-17. https://doi.org/10.4103/0250-474X.102537 Muhammed, M. T., & Aki- Yalcin , E. (2019). Homology modeling in drug discovery: Overview, current applications, and future perspectives. Chemical biology & drug design, 93(1), 12–20. https://www.slideshare.net/slideshow/homology-modelling-75836997/75836997 12

15. Thank you Brita Tamm 502-555-0152 [email protected] www.firstupconsultants.com