Comparing hydropathic interactions between Phenylalanine and Tyrosine

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Presentation transcript:

Comparing hydropathic interactions between Phenylalanine and Tyrosine Sam Portillo BNFO 300 Comparing hydropathic interactions between Phenylalanine and Tyrosine

Homology Modeling – Begins with Amino Acid Sequence

Comparative search to find similar protein in structure database

Predicted Structure

Ahmed et al. (2015) uses “hint!” Developed by Drs. Glen Kellogg and Donald Abraham at VCU

Ahmed et al. (2015) uses “hint!” Developed by Drs. Glen Kellogg and Donald Abraham at VCU Quantifies hydropathic interactions between molecules

Ahmed et al. (2015) uses “hint!” Developed by Drs. Glen Kellogg and Donald Abraham at VCU Quantifies hydropathic interactions between molecules Uses experimental data on previously determined structures

Four classes of interactions “Hydropathy” Four classes of interactions

1. Favorable Hydrophobic Interactions1

1. Favorable Hydrophobic Interactions

2. Unfavorable Hydrophobic Interactions2

2. Unfavorable Hydrophobic Interactions3

3. Favorable Polar Interactions4

4. Unfavorable Polar Interactions5

Visualization of the classes

Ahmed et al. methods Ramachandran plot of 30,000 Tyrosines

Beta sheets form at -135, 135. Alpha helices form from (-90,-15) to (-35,-70)

HINT scoring Box is 20 Å3

HINT basis map Once mapping methods are applied, a 3D representation of the interactions is produced

Map-map similarity is calculated

Clustering with k-means

Tyrosine forms a limited number of 3D conformations

Phenylalanine v. Tyrosine

Chess square d4 predicts alpha helix structure

Highest residue counts in chess squares

Highest residue counts in chess squares

Ulmschneider et al. (2001) calculates Amino acid frequencies in alpha helices

Amino acid frequencies in alpha helices Extracellular Space Cytosol Amino acid frequencies in alpha helices

Amino acid frequencies in alpha helices Extracellular Space Cytosol Amino acid frequencies in alpha helices

Structure conservation among amino acids

References https://dna02.wikispaces.com/file/view/dna_molecule.gif/228169598/396x316/dna_molecule .gif http://myhome.sunyocc.edu/~weiskirl/phospholipid.gif https://www.youtube.com/watch?v=lm-dAvbl330 https://revisionscience.com/a2-level-level-revision/chemistry-level-revision/bonding-and- structure/hydrogen-bonding Adapted from https://snipcademy.com/binf/img/lessons/pairwise-alignments/pam/hvsa.svg Ahmed MH, Koparde VN, Safo MK, Neel Scarsdale J, Kellogg GE. 3D interaction homology: The structurally known rotamers of tyrosine derive from a surprisingly limited set of information- rich hydropathic interaction environments described by maps. Proteins Struct Funct Bioinforma. 2015;83(6):1118-1136. doi:10.1002/prot.24813. Ulmschneider MB, Sansom MSP. Amino acid distributions in integral membrane protein structures. Biochim Biophys Acta. 2001;1512(1):1-14. doi:10.1016/S0005-2736(01)00299-1.