Undergraduate Exercises with Trp Cage Paula Evans, Chet Fornari, Jeff Hansen, Jennifer Inlow, Larry Merkle.

Slides:

Advertisements

Similar presentations

Structural bioinformatics

Advertisements

The Protein Data Bank (PDB)

Phylogeny in Drug Discovery?

Multiple sequence alignment

Protein Tertiary Structure Prediction

Protein domains. Protein domains are structural units (average 160 aa) that share: Function Folding Evolution Proteins normally are multidomain (average.

Structural Bioinformatics R. Sowdhamini National Centre for Biological Sciences Tata Institute of Fundamental Research Bangalore, INDIA.

Tools: Amino acid sequences (PDB, EBI) from many diverse organisms to be provided for students to select about 5-6 organisms representing the three domains.

Multiple Alignment and Phylogenetic Trees Csc 487/687 Computing for Bioinformatics.

Pairwise Sequence Alignment. The most important class of bioinformatics tools – pairwise alignment of DNA and protein seqs. alignment 1alignment 2 Seq.

Comparison of p53 Structure: Wild type vs. mutant What change in wild type p53 may lead to cancer?

Multiple Alignments Motifs/Profiles What is multiple alignment? HOW does one do this? WHY does one do this? What do we mean by a motif or profile? BIO520.

Eidhammer et al. Protein Bioinformatics Chapter 4 1 Multiple Global Sequence Alignment and Phylogenetic trees Inge Jonassen and Ingvar Eidhammer.

STEPHANIE HINTZEN BIOL 471 SIV and HIV: Differences in Diversity and Divergence.

A Mutational Investigation of an HIV Patient’s GP120 Glycoprotein and it’s Implications on CD4 Binding Salita Kaistha Usrinus College, Collegeville PA.

MVKFLFSVIILFFLLSAVGSSARNIEEDGVIRLPSEVKDFINGKNIDDDSVGGTRWAVLI 60 AGSSGYWNYRHQADVCHAYQVLKRGGVKDENIVVFMYDDIALNEENPRPGVIINHPKGED 120 VYAGVPKDYTGRDVTAHNFYSVLLGNKTAVKGGSGKVIDSGPNDHIFIYYSDHGGPGVLG.

Protein Structure & Modeling Biology 224 Instructor: Tom Peavy Nov 18 & 23, 2009

Copyright OpenHelix. No use or reproduction without express written consent1.

Newer method to sequence whole genomes –Uses allyl protecting group: Sequencing by Synthesis.

What is the Evolutionary History and Function of Exendin? Mary Ritke Sandra Davis Octavian Nicolio Angela McKinney-Williams.

Sequence Based Analysis Tutorial March 26, 2004 NIH Proteomics Workshop Lai-Su L. Yeh, Ph.D. Protein Science Team Lead Protein Information Resource at.

Protein Properties Function, structure Residue features Targeting Post-trans modifications BIO520 BioinformaticsJim Lund Reading: Chapter , 11.7,

Chapter 3 The Interrupted Gene.

Hyperthermophile subtilases

Polish Infrastructure for Supporting Computational Science in the European Research Space EUROPEAN UNION Examining Protein Folding Process Simulation and.

Visually Demonstrating the Principles of Protein Folding Bill McClung, Jeff Schwehm, Greg Wolffe.

Protein Sequence Alignment Multiple Sequence Alignment

V diagonal lines give equivalent residues ILS TRIVHVNSILPSTN V I L S T R I V I L P E F S T Sequence A Sequence B Dot Plots, Path Matrices, Score Matrices.

HANDS-ON ConSurf! Web-Server: The ConSurf webserver.

Protein Structure and Function. Proteins are organic compounds made from amino acids held together by peptide bonds.

EBI is an Outstation of the European Molecular Biology Laboratory. A web based integrated search service to understand ligand binding and secondary structure.

Patterns of HIV-1 evolution in individuals with differing rates of CD4 T cell decline Markham RB, Wang WC, Weisstein AE, Wang Z, Munoz A, Templeton A,

Helix-loop-Helix Motif : Simple is Not Boring! Chet Fornari, Jennifer Inlow, Larry Merkle, Barry Muhoberac, Yosi Shibberu.

PDBemotif A web based integrated search service to understand ligand binding and secondary structure properties in macromolecular structures.

Figure 1. Structure of the fly LGR2 gene and the corresponding cDNA sequence. A, Derivation of the fly LGR2 full-length cDNA from the genomic sequence.

Predicting Active Site Residue Annotations in the Pfam Database

Acetylcholine Receptor Binding Toxins

The TNF and TNF Receptor Superfamilies

Kristopher Josephson, Naomi J. Logsdon, Mark R. Walter Immunity

Structure and Signaling Mechanism of Per-ARNT-Sim Domains

LMU Department of Biology

GLUTAMINASE - Phylogenetic tree construction

Protein structure prediction.

Loyola Marymount University

Loyola Marymount University

The MSP domain of MOSPD2 binds the FFAT motif

Figure 2 The p.Lys33Gln mutation eliminates a conserved salt bridge interaction of the matrix network The p.Lys33Gln mutation eliminates a conserved salt.

Volume 19, Issue 12, Pages (December 2011)

The C. elegans SYS-1 Protein Is a Bona Fide β-Catenin

Properties of proteins and residues with frequent hotspot mutations

Selective Dimerization of a C2H2 Zinc Finger Subfamily

Hongwei Wu, Mark W. Maciejewski, Sachiko Takebe, Stephen M. King

Benoit Villiers, Florian Hollfelder Chemistry & Biology

Fig. 1 A single amino acid difference in the ATP-binding domain of GSK3α and GSK3β results in structural and topological differences. A single amino acid.

Volume 14, Issue 11, Pages (November 2006)

Crystal Structures of the BAR-PH and PTB Domains of Human APPL1

Volume 15, Issue 6, Pages (December 2001)

Volume 18, Issue 9, Pages (September 2010)

Michael S. Kuhns, Mark M. Davis Immunity

Alignment of putative chicken HB-EGF to mammalian HB-EGF proteins and the domains of HB-EGF. Alignment of putative chicken HB-EGF to mammalian HB-EGF proteins.

Figure 1 Pedigree and genetic findings

Atomistic Simulations of Viral Insulin Like and Insulin Mimetic Peptides Evan Redfearn and Dr. Harish Vashisth Department of Chemical Engineering, University.

Volume 22, Issue 6, Pages (June 2006)

Annoted amino acid sequence of Aedes aegypti gliotactin (Gli).

Analysis of LC8-binding and nonbinding motifs reveals distinct positional preferences. Analysis of LC8-binding and nonbinding motifs reveals distinct positional.

Kristopher Josephson, Naomi J. Logsdon, Mark R. Walter Immunity

Structural insights based on chimeric Alp4-GCP2 analysis.

Effects of a human FABP7 point mutation on FABP7 protein structure

Benoit Villiers, Florian Hollfelder Chemistry & Biology

Structure of the HLA-DR10 β subunit and ligand binding sites.

Presentation transcript:

Undergraduate Exercises with Trp Cage Paula Evans, Chet Fornari, Jeff Hansen, Jennifer Inlow, Larry Merkle

Background GLP1R Glucagon-like peptide 1 receptor GLP-1 natural peptide ligand of GLP1R Exendin peptide from gila monster venom Trp cage synthetic peptide similar in sequence and structure to Exendin GLP-1 increases glucose-dependent insulin secretion, decreases glucose-dependent glucagon secretion, and and decelerates gastric emptying.

Questions and Hypotheses for Students to Explore 1. How do single-site mutations affect polypeptide structure? If we change specific amino acids, then detectable Structural and Functional alterations will occur. 2. Can we predict general ligand-receptor interactions from structural comparisons, models, and MSA’s? If residues are conserved in the receptors and ligands then these residues are critical for ligand- receptor interactions. 3. Which ligand residues interact with which receptor residues? The chemical properties of the amino acids where the structures of the three ligands overlap will be similar. 4. What are the phylogenetic relationships among these types of receptors? Ligands with similar structures will bind to common domains and motifs.

We can examine and analyze each question/hypothesis in terms of the BioQuest philosophy:

How do single-site mutations affect polypeptide structure? If we change specific amino acids, then detectable structural alterations will occur. Biological Principles chemical properties of amino acids mutations sequence/structure/function Analysis Tools CACHE Deep View and PyMol Data Sets PDB files (Trp Cage, Exendin, GLP-1, receptors)

Explore Deep View as a tool for predicting structural changes that might result from mutation of a given residue. Mutation of Trp to Met in Trp cage

Installed CACHE, loaded PDB file of Trp cage Future Work: Explore CACHE as a tool for predicting structural changes that might result from mutation of a given amino acid residue, and compare these results with the results obtained from DeeP View, MaTras (this study) and from NCBI’s Vast.

Can we predict general ligand-receptor interactions from structural comparisons, models, and MSA’s? If residues are conserved in the receptors and ligands then these residues are critical for ligand- receptor interactions. Biological Principles receptor-ligand interactions intermolecular forces of interaction Analysis Tools CLUSTALW, Bioquest Workbench CACHE, Chimera Data Sets primary sequences of Trp Cage, Exendin, GLP-1

Multiple Sequence Alignment (MSA) of primary sequences of Trp cage, exendin, and GLP-1 reveal conserved residues MSA generated using CLUSTALW (default parameters) at Trp_cage NLYIQWLKDGGPSSGRPPPS Exendin --EGTFTSDLSKQMEEEAVRLFIEWLKNGGPSSGAPPPS GLP-1 HAEGTFTSDVSSYLEGQAAKEFIAWLVKG-----R----. :* **.*

Which ligand residues interact with which receptor residues? The chemical properties of the amino acids where the structures of the three ligands overlap will be similar. Biological Principles chemical properties of amino acids receptor-ligand interactions Analysis Tools Protein Explorer Matras (Kawabata, T. MATRAS: A program for protein 3D structure comparison. Nucleic Acids Res. (2003) 31: ) Data Sets PDB files of 3 ligands

Overlay of 3-dimensional structures of GLP-1 (blue), exendin (red), and Trp cage (green) Figure generated using Matras (use PDB files 1l2y-, 1d0rA, 1jrjA) region of structural overlap

Structural Alignment of 1l2y- (trpCage in blue) with 1d0rA (GLP-1 in red) Figure generated using Matras (use PDB files 1l2y-, 1d0rA)

TrpCage with Exendin TrpCage with GLP-1 GLP-1 with Exendin Other pair-wise views generated by the MaTras program:

Comparison of ligand residues in the region of structural overlap: conserved Lys and hydrophobic patch Trp cage GLP-1 Exendin gray: hydrophobic residues blue: positively- charged residues green: Trp

What are the phylogenetic relationships among these types of receptors? Ligands with similar structures will bind to common domains and motifs. Biological Principles receptor-ligand interactions structure/function Analysis Tools NCBI-CD, Smart, Pfam, InterPro Biology Workbench (tree building algorithms) Data Sets primary sequences of ligands and receptors

Copyright ©2001 by the National Academy of Sciences from West, Anthony P., Jr. et al. (2001) Proc. Natl. Acad. Sci. USA 98: Relation of Methuselah to family B GPCRs and other homologs

Ectodomain (extracellular portion) of Methuselah, a homodimeric receptor related to GLP1R Figure generated using PyMol Potential ligand-binding site highlited in space-fill.