Native contact

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In protein folding, a native contact is a contact between the side chains of two amino acids that are not neighboring in the amino acid sequence (i.e., they are more than four residues apart in the primary sequence in order to remove trivial i to i+4 contacts along alpha helices) but are spatially close in the protein's native state tertiary structure. [1] [2] The fraction of native contacts reproduced in a particular structure is often used as a reaction coordinate for measuring the deviation from the native state of structures produced during molecular dynamics simulations [3] or in benchmarks of protein structure prediction methods. [4]

The contact order is a measure of the locality of a protein's native contacts; [5] that is, the sequence distance between amino acids that form contacts. Proteins with low contact order are thought to fold faster [5] [6] and some may be candidates for downhill folding.

References

  1. Taketomi, H.; Ueda, Y.; Gō, N. (1975). "Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions". International Journal of Peptide and Protein Research. 7 (6): 445–459. doi:10.1111/j.1399-3011.1975.tb02465.x. ISSN   0367-8377. PMID   1201909.
  2. Demharter, Samuel (2014-03-27). "native contacts | Oxford Protein Informatics Group" . Retrieved 2024-01-22.
  3. Best, Robert B.; Hummer, Gerhard; Eaton, William A. (2013-10-29). "Native contacts determine protein folding mechanisms in atomistic simulations". Proceedings of the National Academy of Sciences. 110 (44): 17874–17879. Bibcode:2013PNAS..11017874B. doi: 10.1073/pnas.1311599110 . ISSN   0027-8424. PMC   816414 . PMID   24128758.
  4. Onuchic, José Nelson; Socci, Nicholas D.; Luthey-Schulten, Zaida; Wolynes, Peter G. (1996-12-01). "Protein folding funnels: the nature of the transition state ensemble" . Folding and Design. 1 (6): 441–450. doi:10.1016/S1359-0278(96)00060-0. ISSN   1359-0278. PMID   9080190.
  5. 1 2 Plaxco, Kevin W; Simons, Kim T; Baker, David (1998-04-10). "Contact order, transition state placement and the refolding rates of single domain proteins11Edited by P. E. Wright" . Journal of Molecular Biology. 277 (4): 985–994. doi:10.1006/jmbi.1998.1645. ISSN   0022-2836. PMID   9545386.
  6. Bonneau, Richard; Ruczinski, Ingo; Tsai, Jerry; Baker, David (August 2002). "Contact order and ab initio protein structure prediction". Protein Science. 11 (8): 1937–1944. doi:10.1110/ps.3790102. ISSN   0961-8368. PMC   2373674 . PMID   12142448.