Determine protein structure from amino acid sequence. Ray Luo UC Berkeley EECS
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Transcript of Determine protein structure from amino acid sequence. Ray Luo UC Berkeley EECS
![Page 1: Determine protein structure from amino acid sequence. Ray Luo UC Berkeley EECS](https://reader035.fdocuments.net/reader035/viewer/2022081515/56812f96550346895d9512d8/html5/thumbnails/1.jpg)
UC Berkeley :: EECS :: rluo@uclink
Determine protein structure from amino acid
sequence.Ray Luo
UC Berkeley EECS
![Page 2: Determine protein structure from amino acid sequence. Ray Luo UC Berkeley EECS](https://reader035.fdocuments.net/reader035/viewer/2022081515/56812f96550346895d9512d8/html5/thumbnails/2.jpg)
UC Berkeley :: EECS :: rluo@uclink
Information flows from DNA to RNA to polypeptide string to folded protein.
Polypeptide:amino acidsequence
Folded protein:3D structure
![Page 3: Determine protein structure from amino acid sequence. Ray Luo UC Berkeley EECS](https://reader035.fdocuments.net/reader035/viewer/2022081515/56812f96550346895d9512d8/html5/thumbnails/3.jpg)
UC Berkeley :: EECS :: rluo@uclink
Amino acid sequence encodes the 3D structure and function of a protein.
![Page 4: Determine protein structure from amino acid sequence. Ray Luo UC Berkeley EECS](https://reader035.fdocuments.net/reader035/viewer/2022081515/56812f96550346895d9512d8/html5/thumbnails/4.jpg)
UC Berkeley :: EECS :: rluo@uclink
Comparative methods align sequence against known proteins in a database.
Newprotein
Protein in database
: Protein in database: New proteinAlignment {
![Page 5: Determine protein structure from amino acid sequence. Ray Luo UC Berkeley EECS](https://reader035.fdocuments.net/reader035/viewer/2022081515/56812f96550346895d9512d8/html5/thumbnails/5.jpg)
UC Berkeley :: EECS :: rluo@uclink
De novo methods search for a stable structure by simulating protein folding.
Folded proteinUnfolded protein
Transition state
- Fr
ee e
nerg
y
Reaction coordinate
![Page 6: Determine protein structure from amino acid sequence. Ray Luo UC Berkeley EECS](https://reader035.fdocuments.net/reader035/viewer/2022081515/56812f96550346895d9512d8/html5/thumbnails/6.jpg)
UC Berkeley :: EECS :: rluo@uclink
Most proteins have complicated 3D structures requiring efficient algorithms.
De novo
Comparative
![Page 7: Determine protein structure from amino acid sequence. Ray Luo UC Berkeley EECS](https://reader035.fdocuments.net/reader035/viewer/2022081515/56812f96550346895d9512d8/html5/thumbnails/7.jpg)
UC Berkeley :: EECS :: rluo@uclink
Utilize de novo simulation to support comparative alignment and vice versa.
Proteinfolding
Sequencealignment
SamplingClustering
Cooperative Approach:
![Page 8: Determine protein structure from amino acid sequence. Ray Luo UC Berkeley EECS](https://reader035.fdocuments.net/reader035/viewer/2022081515/56812f96550346895d9512d8/html5/thumbnails/8.jpg)
UC Berkeley :: EECS :: rluo@uclink
Determine protein structure from amino acid sequence using comparative alignment and protein folding simulation.
Proteinfolding
Sequencealignment