메뉴 건너뛰기




Volumn 80, Issue 4, 2012, Pages 991-1002

Asparagine and glutamine differ in their propensities to form specific side chain-backbone hydrogen bonded motifs in proteins

Author keywords

Asparagine residue; Glutamine residue; Neutral polar residues; Protein structures; Side chain backbone hydrogen bonds

Indexed keywords

ASPARAGINE; GLUTAMINE;

EID: 84857728201     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24001     Document Type: Article
Times cited : (29)

References (50)
  • 4
    • 0024290488 scopus 로고
    • Helix signals in proteins
    • Presta LG, Rose GD. Helix signals in proteins. Science 1988; 240: 1632-1641.
    • (1988) Science , vol.240 , pp. 1632-1641
    • Presta, L.G.1    Rose, G.D.2
  • 5
    • 0027204024 scopus 로고
    • Helix stop signals in proteins and peptides: the capping box
    • Harper ET, Rose GD. Helix stop signals in proteins and peptides: the capping box. Biochemistry 1993; 32: 7605-7609.
    • (1993) Biochemistry , vol.32 , pp. 7605-7609
    • Harper, E.T.1    Rose, G.D.2
  • 7
    • 0027212028 scopus 로고
    • Design of helix ends. Amino acid preferences, hydrogen bonding and electrostatic interactions
    • Dasgupta S, Bell JA. Design of helix ends. Amino acid preferences, hydrogen bonding and electrostatic interactions. Int J Pept Protein Res 1993; 41: 499-511.
    • (1993) Int J Pept Protein Res , vol.41 , pp. 499-511
    • Dasgupta, S.1    Bell, J.A.2
  • 8
    • 0024972479 scopus 로고
    • Capping and α-helix stability
    • Serrano L, Fersht AR. Capping and α-helix stability. Nature 1989; 342: 296-299.
    • (1989) Nature , vol.342 , pp. 296-299
    • Serrano, L.1    Fersht, A.R.2
  • 10
    • 0024290472 scopus 로고
    • Amino acid preferences for specific locations at the ends of α-helices
    • Richardson JS, Richardson DC. Amino acid preferences for specific locations at the ends of α-helices. Science 1988; 240: 1648-1652.
    • (1988) Science , vol.240 , pp. 1648-1652
    • Richardson, J.S.1    Richardson, D.C.2
  • 11
    • 0027367977 scopus 로고
    • Helix capping propensities in peptides parallel those in proteins
    • Chakrabarty A, Doig AJ, Baldwin RL. Helix capping propensities in peptides parallel those in proteins. Proc Natl Acad Sci USA 1993; 90: 11332-11336.
    • (1993) Proc Natl Acad Sci USA , vol.90 , pp. 11332-11336
    • Chakrabarty, A.1    Doig, A.J.2    Baldwin, R.L.3
  • 12
    • 0027327319 scopus 로고
    • Common ring motifs in proteins involving asparagine and glutamine amide groups hydrogen bonded to main chain atoms
    • Questel JYL, Morris DG, Maccallum PH, Poet R, Milner-White EJ. Common ring motifs in proteins involving asparagine and glutamine amide groups hydrogen bonded to main chain atoms. J Mol Biol 1993; 231: 888-896.
    • (1993) J Mol Biol , vol.231 , pp. 888-896
    • Questel, J.Y.L.1    Morris, D.G.2    Maccallum, P.H.3    Poet, R.4    Milner-White, E.J.5
  • 13
    • 7244262067 scopus 로고    scopus 로고
    • Mimicry by Asx and ST-turns of the four main types of β-turn in proteins
    • Duddy WJ, Nissink JWM, Allen FH, Milner-White EJ. Mimicry by Asx and ST-turns of the four main types of β-turn in proteins. Protein Sci 2004; 13: 3051-3055.
    • (2004) Protein Sci , vol.13 , pp. 3051-3055
    • Duddy, W.J.1    Nissink, J.W.M.2    Allen, F.H.3    Milner-White, E.J.4
  • 14
    • 0033548459 scopus 로고    scopus 로고
    • A natural grouping of motifs with an aspartate or asparagine residue forming two hydrogen bonds to Residues ahead in sequence: their occurrence at α-helical N-termini and in other situations
    • Wan W-Y, Milner-White EJ. A natural grouping of motifs with an aspartate or asparagine residue forming two hydrogen bonds to Residues ahead in sequence: their occurrence at α-helical N-termini and in other situations. J Mol Biol 1999; 286: 1633-1649.
    • (1999) J Mol Biol , vol.286 , pp. 1633-1649
    • Wan, W.-Y.1    Milner-White, E.J.2
  • 15
    • 0034062925 scopus 로고    scopus 로고
    • Deterministic features of side-chain main chain hydrogen bonds in globular protein structures
    • Eswar N, Ramakrishnan C. Deterministic features of side-chain main chain hydrogen bonds in globular protein structures. Protein Eng 2000; 13: 227-238.
    • (2000) Protein Eng , vol.13 , pp. 227-238
    • Eswar, N.1    Ramakrishnan, C.2
  • 16
    • 0033061876 scopus 로고    scopus 로고
    • Secondary structures without backbone: an analysis of backbone mimicry by polar side chains in protein structures
    • Eswar N, Ramakrishnan C. Secondary structures without backbone: an analysis of backbone mimicry by polar side chains in protein structures. Protein Eng 1999; 12: 447-455.
    • (1999) Protein Eng , vol.12 , pp. 447-455
    • Eswar, N.1    Ramakrishnan, C.2
  • 17
    • 0033104768 scopus 로고    scopus 로고
    • Hydrogen bonds between short polar side chains and peptide backbone: prevalence in proteins and effects on helix-forming propensities
    • Vijayakumar M, Qian H, Zhou HX. Hydrogen bonds between short polar side chains and peptide backbone: prevalence in proteins and effects on helix-forming propensities. Proteins Struct Funct Gen 1999; 34: 497-507.
    • (1999) Proteins Struct Funct Gen , vol.34 , pp. 497-507
    • Vijayakumar, M.1    Qian, H.2    Zhou, H.X.3
  • 18
    • 0027988211 scopus 로고
    • The role of side-chain hydrogen bonds in the formation and stabilization of secondary structure in soluble proteins
    • Bordo D, Argos P. The role of side-chain hydrogen bonds in the formation and stabilization of secondary structure in soluble proteins. J Mol Biol 1994; 243: 504-519.
    • (1994) J Mol Biol , vol.243 , pp. 504-519
    • Bordo, D.1    Argos, P.2
  • 19
    • 0019443447 scopus 로고
    • The anatomy and taxonomy of protein structure
    • Richardson JS. The anatomy and taxonomy of protein structure. Adv Protein Chem 1981; 34; 167-339.
    • (1981) Adv Protein Chem , vol.34 , pp. 167-339
    • Richardson, J.S.1
  • 20
    • 0027530219 scopus 로고
    • Termination of right-handed helices in proteins by residues in left-handed helical conformation
    • Nagarajaram HA, Sowdhamini R, Ramakrishnan C. Balaram P. Termination of right-handed helices in proteins by residues in left-handed helical conformation. FEBS Lett 1993; 321: 79-83.
    • (1993) FEBS Lett , vol.321 , pp. 79-83
    • Nagarajaram, H.A.1    Sowdhamini, R.2    Ramakrishnan, C.3    Balaram, P.4
  • 22
    • 0035882544 scopus 로고    scopus 로고
    • Role of non-Glycine residues in left-handed helical conformation for the conformational stability of human lysozyme
    • Takano K, Yamagata Y, Yutani K. Role of non-Glycine residues in left-handed helical conformation for the conformational stability of human lysozyme. Proteins: Struct Funct Gen 2001; 44: 233-243.
    • (2001) Proteins: Struct Funct Gen , vol.44 , pp. 233-243
    • Takano, K.1    Yamagata, Y.2    Yutani, K.3
  • 26
    • 0038100303 scopus 로고
    • Predicted conformations for the immunodominant region of the circumsporozoite protein of the human malaria parasite Plasmodium falciparum
    • Gibson KD, Scheraga HA. Predicted conformations for the immunodominant region of the circumsporozoite protein of the human malaria parasite Plasmodium falciparum. Proc Natl Acad Sci USA 1986; 83: 5649-5653.
    • (1986) Proc Natl Acad Sci USA , vol.83 , pp. 5649-5653
    • Gibson, K.D.1    Scheraga, H.A.2
  • 27
    • 0033080367 scopus 로고    scopus 로고
    • Glutamine repeats and neurodegenerative disorders
    • Perutz MF. Glutamine repeats and neurodegenerative disorders. Mol Aspects Trends Biochem Sci 1999; 24: 58-63.
    • (1999) Mol Aspects Trends Biochem Sci , vol.24 , pp. 58-63
    • Perutz, M.F.1
  • 33
    • 68149124204 scopus 로고    scopus 로고
    • Structural effects of a dimer interface mutation on catalytic activity of triosephosphate isomerase. The role of conserved residues and complementary mutations
    • Banerjee M, Balaram H, Balaram P. Structural effects of a dimer interface mutation on catalytic activity of triosephosphate isomerase. The role of conserved residues and complementary mutations. FEBS J 2009; 276: 4169-4183.
    • (2009) FEBS J , vol.276 , pp. 4169-4183
    • Banerjee, M.1    Balaram, H.2    Balaram, P.3
  • 34
    • 0037422593 scopus 로고    scopus 로고
    • Optimal alignment for enzymatic proton transfer: structure of the Michaelis complex of triosephosphate isomerase at 1.2Å resolution
    • Jogl G, Rozovsky S, McDermott AE, Tong L. Optimal alignment for enzymatic proton transfer: structure of the Michaelis complex of triosephosphate isomerase at 1.2Å resolution. Proc Natl Acad Sci USA 2003; 100: 50-55.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 50-55
    • Jogl, G.1    Rozovsky, S.2    McDermott, A.E.3    Tong, L.4
  • 36
    • 0027146064 scopus 로고
    • The crystal structure of an engineered monomeric triosephosphate isomerase, monoTIM: the correct modelling of an eight-residue loop
    • Borchert TV, Abagyan R, Kishan KV, Zeelan JP, Wierenga RK. The crystal structure of an engineered monomeric triosephosphate isomerase, monoTIM: the correct modelling of an eight-residue loop. Structure 1993; 1: 205-213.
    • (1993) Structure , vol.1 , pp. 205-213
    • Borchert, T.V.1    Abagyan, R.2    Kishan, K.V.3    Zeelan, J.P.4    Wierenga, R.K.5
  • 37
    • 77952752455 scopus 로고    scopus 로고
    • On the evolutionary conservation of hydrogen bonds made by buried polar amino acids: the hidden joists, braces and trusses of protein architecture
    • Worth CL, Blundell T. On the evolutionary conservation of hydrogen bonds made by buried polar amino acids: the hidden joists, braces and trusses of protein architecture. BMC Evol Biol 2010; 10: 161-171.
    • (2010) BMC Evol Biol , vol.10 , pp. 161-171
    • Worth, C.L.1    Blundell, T.2
  • 38
    • 0029017638 scopus 로고
    • The application of hydrogen bonding analysis in X-ray crystallography to help orientate asparagin, glutamine and histidine side chains
    • McDonald IK, Thornton JM. The application of hydrogen bonding analysis in X-ray crystallography to help orientate asparagin, glutamine and histidine side chains. Protein Eng 1994; 8: 217-224.
    • (1994) Protein Eng , vol.8 , pp. 217-224
    • McDonald, I.K.1    Thornton, J.M.2
  • 39
    • 0033582329 scopus 로고    scopus 로고
    • Asparagine and glutamine rotamers: B-factor cutoff and correction of amide flips yield distinct clustering
    • Lovell SC, Word JM, Richardson JS, Richardson DC. Asparagine and glutamine rotamers: B-factor cutoff and correction of amide flips yield distinct clustering. Proc Natl Acad Sci USA 1999; 96: 400-405.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 400-405
    • Lovell, S.C.1    Word, J.M.2    Richardson, J.S.3    Richardson, D.C.4
  • 40
    • 0033614004 scopus 로고    scopus 로고
    • Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation
    • Word JM, Lovell SC, Richardson JS, Richardson DC. Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J Mol Biol 1999; 285: 1735-1747.
    • (1999) J Mol Biol , vol.285 , pp. 1735-1747
    • Word, J.M.1    Lovell, S.C.2    Richardson, J.S.3    Richardson, D.C.4
  • 41
    • 34547593171 scopus 로고    scopus 로고
    • NA-Flipper: recognition and correction of erroneous asparagine and glutamine side-chain rotamers in protein structures
    • Weichenberger CX, Sippl MJ. NA-Flipper: recognition and correction of erroneous asparagine and glutamine side-chain rotamers in protein structures. Nucleic Acids Res 2007; 35: W403-W406.
    • (2007) Nucleic Acids Res , vol.35
    • Weichenberger, C.X.1    Sippl, M.J.2
  • 42
    • 0014347799 scopus 로고
    • Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units
    • Venkatachalam CM. Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units. Biopolymers 1968; 6: 1425-1436.
    • (1968) Biopolymers , vol.6 , pp. 1425-1436
    • Venkatachalam, C.M.1
  • 43
    • 0024279235 scopus 로고
    • Analysis and prediction of the different types of β-turn in proteins
    • Wilmot CM. Thornton JM. Analysis and prediction of the different types of β-turn in proteins. J Mol Biol 1988; 203: 221-232.
    • (1988) J Mol Biol , vol.203 , pp. 221-232
    • Wilmot, C.M.1    Thornton, J.M.2
  • 45
    • 0001428018 scopus 로고
    • L -conformation at the ends of helices
    • JaenickeR, editor. North-Holland New York: Elsevier;
    • L -conformation at the ends of helices. In: Jaenicke R, editor. Protein folding. North-Holland New York: Elsevier; 1980. pp 53-61.
    • (1980) Protein folding , pp. 53-61
    • Schellman, C.1
  • 46
    • 0032488824 scopus 로고    scopus 로고
    • Stereochemical punctuation marks in protein structures: glycine and proline containing helix stop signals
    • Gunasekaran K, Nagarajaram HA, Ramakrishnan C, Balaram P. Stereochemical punctuation marks in protein structures: glycine and proline containing helix stop signals. J Mol Biol 1998; 275: 917-932.
    • (1998) J Mol Biol , vol.275 , pp. 917-932
    • Gunasekaran, K.1    Nagarajaram, H.A.2    Ramakrishnan, C.3    Balaram, P.4
  • 47
    • 33645450694 scopus 로고    scopus 로고
    • Crystal structure of an NPNA-repeat motif from the circumsporozoite protein of malaria parasite, Plasmodium falciparum
    • Ghasparin A, Moehle K, Linden A, Robinson JA. Crystal structure of an NPNA-repeat motif from the circumsporozoite protein of malaria parasite, Plasmodium falciparum. Chem Commun 2006: 174-176.
    • Chem Commun , vol.2006 , pp. 174-176
    • Ghasparin, A.1    Moehle, K.2    Linden, A.3    Robinson, J.A.4
  • 49
    • 77952335945 scopus 로고    scopus 로고
    • Spontaneous formation of polyglutamine nanotubes with molecular dynamics simulations
    • Laghaei R, Mousseau N. Spontaneous formation of polyglutamine nanotubes with molecular dynamics simulations. J Chem Phys 2010; 132: 165102-165109.
    • (2010) J Chem Phys , vol.132 , pp. 165102-165109
    • Laghaei, R.1    Mousseau, N.2
  • 50
    • 0141765883 scopus 로고    scopus 로고
    • Fabrication of novel biomaterials through molecular self-assembly
    • Zhang S. Fabrication of novel biomaterials through molecular self-assembly. Nature Biotech 2003; 21: 1171-1178.
    • (2003) Nature Biotech , vol.21 , pp. 1171-1178
    • Zhang, S.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.