lecture3 - Bioinformatics 2 lecture 3 Structure...

Info icon This preview shows pages 1–8. Sign up to view the full content.

View Full Document Right Arrow Icon
Bioinformatics 2 -- lecture 3 Structure classification TOPS Domains
Image of page 1

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full Document Right Arrow Icon
CATH • Class • Architecture • Topology • Homology http://www.biochem.ucl.ac.uk/bsm/cath_new/index.html
Image of page 2
Structure classification: SCOP Contains information about classification of protein structures and within that classification, their sequences • http://scop.berkeley.edu
Image of page 3

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full Document Right Arrow Icon
Structure classification: SCOP (1) class (2) fold (3) superfamily (4) family (5) protein (6) species global characteristics (no evolutionary relation) Similar “topology” . Distant evolutionary cousins? Clear structural homology Clear sequence homology functionally identical unique sequences http://scop.berkeley.edu
Image of page 4
protein classes 1. all α (126) 2. all β (81) 3. α / β (87) 4. α + β (151) 5. multidomain (21) 6. membrane (21) 7. small (10) 8. coiled coil (4) 9. low-resolution (4) 10. peptides (61) 11. designed proteins (17) number of sub-categories (126) possibly not complete, or erroneous Not true classes
Image of page 5

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full Document Right Arrow Icon
class: α / β proteins Folds : TIM-barrel (22) swivelling beta/beta/alpha domain (5) spoIIaa-like (2) flavodoxin-like (10) restriction endonuclease-like (2) ribokinase-like (2) chelatase-like (2) Mainly parallel beta sheets (beta-alpha-beta units) Many folds have historical names. “TIM” barrel was first seen in TIM. These classifications are done by eye, mostly.
Image of page 6
fold: flavodoxin-like Superfamilies: 1.Catalase, C-terminal domain (1) 2.CheY-like (1) 3.Succinyl-CoA synthetase domains (1) 4.Flavoproteins (3) 5.Cobalamin (vitamin B12)-binding domain (1) 6.Ornithine decarboxylase N-terminal "wing" domain (1) 7.Cutinase-like (1) 8.Esterase/acetylhydrolase (2) 9.Formate/glycerate dehydrogenase catalytic domain-like (3)
Image of page 7

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full Document Right Arrow Icon
Image of page 8
This is the end of the preview. Sign up to access the rest of the document.

{[ snackBarMessage ]}

What students are saying

  • Left Quote Icon

    As a current student on this bumpy collegiate pathway, I stumbled upon Course Hero, where I can find study resources for nearly all my courses, get online help from tutors 24/7, and even share my old projects, papers, and lecture notes with other students.

    Student Picture

    Kiran Temple University Fox School of Business ‘17, Course Hero Intern

  • Left Quote Icon

    I cannot even describe how much Course Hero helped me this summer. It’s truly become something I can always rely on and help me. In the end, I was not only able to survive summer classes, but I was able to thrive thanks to Course Hero.

    Student Picture

    Dana University of Pennsylvania ‘17, Course Hero Intern

  • Left Quote Icon

    The ability to access any university’s resources through Course Hero proved invaluable in my case. I was behind on Tulane coursework and actually used UCLA’s materials to help me move forward and get everything together on time.

    Student Picture

    Jill Tulane University ‘16, Course Hero Intern