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Wikipedia

Omega loop

January 01, 1970

The omega loop[1][2] is a non-regular protein structural motif, consisting of a loop of six or more amino acid residues and any amino acid sequence. The defining characteristic is that residues that make up the beginning and end of the loop are close together in space with no intervening lengths of regular secondary structural motifs. It is named after its shape, which resembles the upper-case Greek letter Omega (Ω).

Structure edit

Omega loops, being non-regular, non-repeating secondary structural units, have a variety of three-dimensional shapes. Omega loop shapes are analyzed to identify recurring patterns in dihedral angles and overall loop shape to help identify potential roles in protein folding and function.[3][4]

Since loops are almost always at the protein surface, it is often assumed that these structures are flexible; however, different omega loops exhibit ranges of flexibility across different time scales of protein motion and have been identified as playing a role in the folding of some proteins, including HIV-1 reverse transcriptase;[5][6] cytochrome c;[7][8] and nucleases.[9][10]

Function edit

Omega loops can contribute to protein function. For example, omega loops can help stabilize interactions between protein and ligand, such as in the enzyme triose phosphate isomerase,[11] and can directly affect protein function in other enzymes.[12][13] A heritable coagulation disorder is caused by a single-site mutation in an omega loop of protein C.[14]

Likewise, omega loops play an interesting role in the function of the beta-lactamases: mutations in the "omega loop region" of a beta-lactamase can change its specific function and substrate profile,[15][16][17] perhaps due to an important functional role of the correlated dynamics of the region.[18]

Cytochrome c edit

Omega loops have long been recognized also for their importance in the function and folding of the protein cytochrome c, contributing both key functional residues and well as important dynamic properties.[19][20][21] Many researchers have studied omega loop function and dynamics in specific protein systems using a so-called "loop swap" approach, in which loops are swapped between (usually) homologous proteins.[22][23][24]

References edit

  1. ^ Leszczynski, JF; Rose, GD (14 Nov 1986). "Loops in globular proteins: a novel category of secondary structure". Science. 234 (4778): 849–855. Bibcode:1986Sci...234..849L. doi:10.1126/science.3775366. PMID 3775366.
  2. ^ Fetrow, JS (June 1995). "Omega loops: nonregular secondary structures significant in protein function and stability". FASEB J. 9 (9): 708–17. doi:10.1096/fasebj.9.9.7601335. PMID 7601335. S2CID 23775489.
  3. ^ Pal, M; Dasgupta, S (1 Jun 2003). "The nature of the turn in omega loops of proteins". Proteins. 51 (4): 591–606. doi:10.1002/prot.10376. PMID 12784218. S2CID 44815936.
  4. ^ Dhar, J; Chakrabarti, P (Jun 2015). "Defining the loop structures in proteins based on composite β-turn mimics". Protein Eng Des Sel. 28 (6): 153–61. doi:10.1093/protein/gzv017. PMID 25870305.
  5. ^ Mager, PP (Dec 1996). "Molecular simulation of the folding patterns of the omega-loop (Tyr181 to Tyr188) of HIV-1 reverse transcriptase". Drug des Discov. 14 (3): 213–23. PMID 9017364.
  6. ^ Mager, PP; Walther, H (Dec 1996). "A hydrophilic omega-loop (Tyr181 to Tyr188) in the nonsubstrate binding area of HIV-1 reverse transcriptase". Drug des Discov. 14 (3): 225–39. PMID 9017365.
  7. ^ Maity, H; Rumbley, JN; Englander, SW (1 May 2006). "Functional role of a protein foldon--an Omega-loop foldon controls the alkaline transition in ferricytochrome c". Proteins. 63 (2): 349–55. CiteSeerX 10.1.1.596.3784. doi:10.1002/prot.20757. PMID 16287119. S2CID 38183696.
  8. ^ Caroppi, P; Sinibaldi, F; Santoni, E; Howes, BD; Fiorucci, L; Ferri, T; Ascoli, F; Smulevich, G; Santucci, R (Dec 2004). "The 40s Omega-loop plays a critical role in the stability and the alkaline conformational transition of cytochrome c". J Biol Inorg Chem. 9 (8): 997–1006. doi:10.1007/s00775-004-0601-9. hdl:2108/34631. PMID 15503233. S2CID 2130725.
  9. ^ Vu, ND; Feng, H; Bai, Y (30 Mar 2004). "The folding pathway of barnase: the rate-limiting transition state and a hidden intermediate under native conditions". Biochemistry. 43 (12): 3346–56. doi:10.1021/bi0362267. PMID 15035606.
  10. ^ Wang, X; Wang, M; Tong, Y; Shan, L; Wang, J (Oct 2006). "Probing the folding capacity and residual structures in 1-79 residues fragment of staphylococcal nuclease by biophysical and NMR methods". Biochimie. 88 (10): 1343–55. doi:10.1016/j.biochi.2006.05.002. PMID 17045725.
  11. ^ Xiang, J; Jung, JY; Sampson, NS (14 Sep 2004). "Entropy effects on protein hinges: the reaction catalyzed by triosephosphate isomerase". Biochemistry. 43 (36): 11436–45. doi:10.1021/bi049208d. PMID 15350130.
  12. ^ Neuhaus, FC (Sep 2011). "Role of the omega loop in specificity determination in subsite 2 of the D-alanine:D-alanine (D-lactate) ligase from Leuconostoc mesenteroides: a molecular docking study". J Mol Graph Model. 30: 31–7. doi:10.1016/j.jmgm.2011.06.002. PMID 21727015.
  13. ^ Sampson, NS; Kass, IJ; Ghoshroy, KB (21 Apr 1998). "Assessment of the role of an omega loop of cholesterol oxidase: a truncated loop mutant has altered substrate specificity". Biochemistry. 37 (16): 5770–8. doi:10.1021/bi973067g. PMID 9548964.
  14. ^ Preston, RJ; Morse, C; Murden, SL; Brady, SK; O'Donnell, JS; Mumford, AD (Mar 2009). "The protein C omega-loop substitution Asn2Ile is associated with reduced protein C anticoagulant activity". Br J Haematol. 144 (6): 946–53. doi:10.1111/j.1365-2141.2008.07550.x. PMID 19133979. S2CID 1618500.
  15. ^ Levitt, PS; Papp-Wallace, KM; Taracila, MA; Hujer, AM; Winkler, ML; Smith, KM; Xu, Y; Harris, ME; Bonomo, RA (14 Sep 2013). "Exploring the role of a conserved class A residue in the Ω-Loop of KPC-2 β-lactamase: a mechanism for ceftazidime hydrolysis". J Biol Chem. 287 (38): 31783–93. doi:10.1074/jbc.M112.348540. PMC 3442512. PMID 22843686.
  16. ^ Stojanoski, V; Chow, DC; Hu, L; Sankaran, B; Gilbert, HF; Prasad, BV; Palzkill, T (17 Apr 2015). "A triple mutant in the Ω-loop of TEM-1 β-lactamase changes the substrate profile via a large conformational change and an altered general base for catalysis". J Biol Chem. 290 (16): 10382–94. doi:10.1074/jbc.M114.633438. PMC 4400348. PMID 25713062.
  17. ^ Dutta, M; Kar, D; Bansal, A; Chakraborty, S; Ghosh, AS (Apr 2015). "A single amino acid substitution in the Ω-like loop of E. coli PBP5 disrupts its ability to maintain cell shape and intrinsic beta-lactam resistance". Microbiology. 161 (Pt 4): 895–902. doi:10.1099/mic.0.000052. PMID 25667006.
  18. ^ Brown, JR; Livesay, DR (27 May 2015). "Flexibility Correlation between Active Site Regions Is Conserved across Four AmpC β-Lactamase Enzymes". PLOS ONE. 10 (5): e0125832. Bibcode:2015PLoSO..1025832B. doi:10.1371/journal.pone.0125832. PMC 4446314. PMID 26018804.
  19. ^ McClelland, LJ; Seagraves, SM; Khan, MK; Cherney, MM; Bandi, S; Culbertson, JE; Bowler, BE (Jul 2015). "The response of Ω-loop D dynamics to truncation of trimethyllysine 72 of yeast iso-1-cytochrome c depends on the nature of loop deformation". J Biol Inorg Chem. 20 (5): 805–19. doi:10.1007/s00775-015-1267-1. PMC 4485566. PMID 25948392.
  20. ^ Krishna, MM; Lin, Y; Rumbley, JN; Englander, SW (1 Aug 2003). "Cooperative omega loops in cytochrome c: role in folding and function". J Mol Biol. 331 (1): 29–36. doi:10.1016/s0022-2836(03)00697-1. PMID 12875833.
  21. ^ Fetrow, JS; Dreher, U; Wiland, DJ; Schaak, DL; Boose, TL (Apr 1998). "Mutagenesis of histidine 26 demonstrates the importance of loop-loop and loop-protein interactions for the function of iso-1-cytochrome c". Protein Sci. 7 (4): 994–1005. doi:10.1002/pro.5560070417. PMC 2143970. PMID 9568906.
  22. ^ Takehara, S; Onda, M; Zhang, J; Nishiyama, M; Yang, X; Mikami, B; Lomas, DA (24 Apr 2009). "The 2.1-A crystal structure of native neuroserpin reveals unique structural elements that contribute to conformational instability". J Mol Biol. 388 (1): 11–20. doi:10.1016/j.jmb.2009.03.007. PMID 19285087.
  23. ^ Murphy, ME; Fetrow, JS; Burton, RE; Brayer, GD (Sep 1993). "The structure and function of omega loop A replacements in cytochrome c". Protein Sci. 2 (9): 1429–40. doi:10.1002/pro.5560020907. PMC 2142463. PMID 8401228.
  24. ^ Fetrow, JS; Cardillo, TS; Sherman, F (1989). "Deletions and replacements of omega loops in yeast iso-1-cytochrome c". Proteins. 6 (4): 372–81. doi:10.1002/prot.340060404. PMID 2560195. S2CID 25525703.

January 01, 1970
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The omega loop 1 2 is a non regular protein structural motif consisting of a loop of six or more amino acid residues and any amino acid sequence The defining characteristic is that residues that make up the beginning and end of the loop are close together in space with no intervening lengths of regular secondary structural motifs It is named after its shape which resembles the upper case Greek letter Omega W Contents 1 Structure 2 Function 2 1 Cytochrome c 3 ReferencesStructure editOmega loops being non regular non repeating secondary structural units have a variety of three dimensional shapes Omega loop shapes are analyzed to identify recurring patterns in dihedral angles and overall loop shape to help identify potential roles in protein folding and function 3 4 Since loops are almost always at the protein surface it is often assumed that these structures are flexible however different omega loops exhibit ranges of flexibility across different time scales of protein motion and have been identified as playing a role in the folding of some proteins including HIV 1 reverse transcriptase 5 6 cytochrome c 7 8 and nucleases 9 10 Function editOmega loops can contribute to protein function For example omega loops can help stabilize interactions between protein and ligand such as in the enzyme triose phosphate isomerase 11 and can directly affect protein function in other enzymes 12 13 A heritable coagulation disorder is caused by a single site mutation in an omega loop of protein C 14 Likewise omega loops play an interesting role in the function of the beta lactamases mutations in the omega loop region of a beta lactamase can change its specific function and substrate profile 15 16 17 perhaps due to an important functional role of the correlated dynamics of the region 18 Cytochrome c edit Omega loops have long been recognized also for their importance in the function and folding of the protein cytochrome c contributing both key functional residues and well as important dynamic properties 19 20 21 Many researchers have studied omega loop function and dynamics in specific protein systems using a so called loop swap approach in which loops are swapped between usually homologous proteins 22 23 24 References edit Leszczynski JF Rose GD 14 Nov 1986 Loops in globular proteins a novel category of secondary structure Science 234 4778 849 855 Bibcode 1986Sci 234 849L doi 10 1126 science 3775366 PMID 3775366 Fetrow JS June 1995 Omega loops nonregular secondary structures significant in protein function and stability FASEB J 9 9 708 17 doi 10 1096 fasebj 9 9 7601335 PMID 7601335 S2CID 23775489 Pal M Dasgupta S 1 Jun 2003 The nature of the turn in omega loops of proteins Proteins 51 4 591 606 doi 10 1002 prot 10376 PMID 12784218 S2CID 44815936 Dhar J Chakrabarti P Jun 2015 Defining the loop structures in proteins based on composite b turn mimics Protein Eng Des Sel 28 6 153 61 doi 10 1093 protein gzv017 PMID 25870305 Mager PP Dec 1996 Molecular simulation of the folding patterns of the omega loop Tyr181 to Tyr188 of HIV 1 reverse transcriptase Drug des Discov 14 3 213 23 PMID 9017364 Mager PP Walther H Dec 1996 A hydrophilic omega loop Tyr181 to Tyr188 in the nonsubstrate binding area of HIV 1 reverse transcriptase Drug des Discov 14 3 225 39 PMID 9017365 Maity H Rumbley JN Englander SW 1 May 2006 Functional role of a protein foldon an Omega loop foldon controls the alkaline transition in ferricytochrome c Proteins 63 2 349 55 CiteSeerX 10 1 1 596 3784 doi 10 1002 prot 20757 PMID 16287119 S2CID 38183696 Caroppi P Sinibaldi F Santoni E Howes BD Fiorucci L Ferri T Ascoli F Smulevich G Santucci R Dec 2004 The 40s Omega loop plays a critical role in the stability and the alkaline conformational transition of cytochrome c J Biol Inorg Chem 9 8 997 1006 doi 10 1007 s00775 004 0601 9 hdl 2108 34631 PMID 15503233 S2CID 2130725 Vu ND Feng H Bai Y 30 Mar 2004 The folding pathway of barnase the rate limiting transition state and a hidden intermediate under native conditions Biochemistry 43 12 3346 56 doi 10 1021 bi0362267 PMID 15035606 Wang X Wang M Tong Y Shan L Wang J Oct 2006 Probing the folding capacity and residual structures in 1 79 residues fragment of staphylococcal nuclease by biophysical and NMR methods Biochimie 88 10 1343 55 doi 10 1016 j biochi 2006 05 002 PMID 17045725 Xiang J Jung JY Sampson NS 14 Sep 2004 Entropy effects on protein hinges the reaction catalyzed by triosephosphate isomerase Biochemistry 43 36 11436 45 doi 10 1021 bi049208d PMID 15350130 Neuhaus FC Sep 2011 Role of the omega loop in specificity determination in subsite 2 of the D alanine D alanine D lactate ligase from Leuconostoc mesenteroides a molecular docking study J Mol Graph Model 30 31 7 doi 10 1016 j jmgm 2011 06 002 PMID 21727015 Sampson NS Kass IJ Ghoshroy KB 21 Apr 1998 Assessment of the role of an omega loop of cholesterol oxidase a truncated loop mutant has altered substrate specificity Biochemistry 37 16 5770 8 doi 10 1021 bi973067g PMID 9548964 Preston RJ Morse C Murden SL Brady SK O Donnell JS Mumford AD Mar 2009 The protein C omega loop substitution Asn2Ile is associated with reduced protein C anticoagulant activity Br J Haematol 144 6 946 53 doi 10 1111 j 1365 2141 2008 07550 x PMID 19133979 S2CID 1618500 Levitt PS Papp Wallace KM Taracila MA Hujer AM Winkler ML Smith KM Xu Y Harris ME Bonomo RA 14 Sep 2013 Exploring the role of a conserved class A residue in the W Loop of KPC 2 b lactamase a mechanism for ceftazidime hydrolysis J Biol Chem 287 38 31783 93 doi 10 1074 jbc M112 348540 PMC 3442512 PMID 22843686 Stojanoski V Chow DC Hu L Sankaran B Gilbert HF Prasad BV Palzkill T 17 Apr 2015 A triple mutant in the W loop of TEM 1 b lactamase changes the substrate profile via a large conformational change and an altered general base for catalysis J Biol Chem 290 16 10382 94 doi 10 1074 jbc M114 633438 PMC 4400348 PMID 25713062 Dutta M Kar D Bansal A Chakraborty S Ghosh AS Apr 2015 A single amino acid substitution in the W like loop of E coli PBP5 disrupts its ability to maintain cell shape and intrinsic beta lactam resistance Microbiology 161 Pt 4 895 902 doi 10 1099 mic 0 000052 PMID 25667006 Brown JR Livesay DR 27 May 2015 Flexibility Correlation between Active Site Regions Is Conserved across Four AmpC b Lactamase Enzymes PLOS ONE 10 5 e0125832 Bibcode 2015PLoSO 1025832B doi 10 1371 journal pone 0125832 PMC 4446314 PMID 26018804 McClelland LJ Seagraves SM Khan MK Cherney MM Bandi S Culbertson JE Bowler BE Jul 2015 The response of W loop D dynamics to truncation of trimethyllysine 72 of yeast iso 1 cytochrome c depends on the nature of loop deformation J Biol Inorg Chem 20 5 805 19 doi 10 1007 s00775 015 1267 1 PMC 4485566 PMID 25948392 Krishna MM Lin Y Rumbley JN Englander SW 1 Aug 2003 Cooperative omega loops in cytochrome c role in folding and function J Mol Biol 331 1 29 36 doi 10 1016 s0022 2836 03 00697 1 PMID 12875833 Fetrow JS Dreher U Wiland DJ Schaak DL Boose TL Apr 1998 Mutagenesis of histidine 26 demonstrates the importance of loop loop and loop protein interactions for the function of iso 1 cytochrome c Protein Sci 7 4 994 1005 doi 10 1002 pro 5560070417 PMC 2143970 PMID 9568906 Takehara S Onda M Zhang J Nishiyama M Yang X Mikami B Lomas DA 24 Apr 2009 The 2 1 A crystal structure of native neuroserpin reveals unique structural elements that contribute to conformational instability J Mol Biol 388 1 11 20 doi 10 1016 j jmb 2009 03 007 PMID 19285087 Murphy ME Fetrow JS Burton RE Brayer GD Sep 1993 The structure and function of omega loop A replacements in cytochrome c Protein Sci 2 9 1429 40 doi 10 1002 pro 5560020907 PMC 2142463 PMID 8401228 Fetrow JS Cardillo TS Sherman F 1989 Deletions and replacements of omega loops in yeast iso 1 cytochrome c Proteins 6 4 372 81 doi 10 1002 prot 340060404 PMID 2560195 S2CID 25525703 Retrieved from https en wikipedia org w index php title Omega loop amp oldid 1215824779, wikipedia, wiki, book, books, library,

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