메뉴 건너뛰기




Volumn 2013, Issue , 2013, Pages

Interplay between peptide bond geometrical parameters in nonglobular structural contexts

Author keywords

[No Author keywords available]

Indexed keywords

AMYLOID; COLLAGEN; COLLAGEN LIKE PEPTIDE; GLOBULAR PROTEIN; MEMBRANE PROTEIN; PEPTIDE; PROTEIN; UNCLASSIFIED DRUG; WATER SOLUBLE PROTEIN; AMYLOID PROTEIN; WATER;

EID: 84896066400     PISSN: 23146133     EISSN: 23146141     Source Type: Journal    
DOI: 10.1155/2013/326914     Document Type: Article
Times cited : (13)

References (35)
  • 1
    • 0019443447 scopus 로고
    • The anatomy and taxonomy of protein structure
    • 2-s2.0-0019443447 10.1016/S0065-3233(08)60520-3
    • Richardson J. S., The anatomy and taxonomy of protein structure. Advances in Protein Chemistry 1981 34 167 339 2-s2.0-0019443447 10.1016/S0065-3233(08) 60520-3
    • (1981) Advances in Protein Chemistry , vol.34 , pp. 167-339
    • Richardson, J.S.1
  • 2
    • 0030010605 scopus 로고    scopus 로고
    • Experimentally observed conformation-dependent geometry and hidden strain in proteins
    • Karplus P. A., Experimentally observed conformation-dependent geometry and hidden strain in proteins. Protein Science 1996 5 7 1406 1420 2-s2.0-0030010605 (Pubitemid 26239448)
    • (1996) Protein Science , vol.5 , Issue.7 , pp. 1406-1420
    • Karplus, P.A.1
  • 3
    • 0034737316 scopus 로고    scopus 로고
    • The ultrahigh resolution crystal structure of ribonuclease A containing an isoaspartyl residue: Hydration and sterochemical analysis
    • 2-s2.0-0034737316 10.1006/jmbi.2000.3597
    • Esposito L., Vitagliano L., Sica F., Sorrentino G., Zagari A., Mazzarella L., The ultrahigh resolution crystal structure of ribonuclease A containing an isoaspartyl residue: hydration and sterochemical analysis. Journal of Molecular Biology 2000 297 3 713 732 2-s2.0-0034737316 10.1006/jmbi.2000.3597
    • (2000) Journal of Molecular Biology , vol.297 , Issue.3 , pp. 713-732
    • Esposito, L.1    Vitagliano, L.2    Sica, F.3    Sorrentino, G.4    Zagari, A.5    Mazzarella, L.6
  • 4
    • 0034461614 scopus 로고    scopus 로고
    • Experimental evidence for the correlation of bond distances in peptide groups detected in ultrahigh-resolution protein structures
    • Esposito L., Vitagliano L., Zagari A., Mazzarella L., Experimental evidence for the correlation of bond distances in peptide groups detected in ultrahigh-resolution protein structures. Protein Engineering 2000 13 12 825 828 2-s2.0-0034461614 (Pubitemid 32233941)
    • (2000) Protein Engineering , vol.13 , Issue.12 , pp. 825-828
    • Esposito, L.1    Vitagliano, L.2    Zagari, A.3    Mazzarella, L.4
  • 5
    • 14744285538 scopus 로고    scopus 로고
    • Correlation between ω and ψ dihedral angles in protein structures
    • DOI 10.1016/j.jmb.2005.01.065
    • Esposito L., de Simone A., Zagari A., Vitagliano L., Correlation between ω and ψ dihedral angles in protein structures. Journal of Molecular Biology 2005 347 3 483 487 2-s2.0-14744285538 10.1016/j.jmb.2005.01.065 (Pubitemid 40332358)
    • (2005) Journal of Molecular Biology , vol.347 , Issue.3 , pp. 483-487
    • Esposito, L.1    De Simone, A.2    Zagari, A.3    Vitagliano, L.4
  • 6
    • 0036527061 scopus 로고    scopus 로고
    • Recent advances in atomic resolution protein crystallography
    • Esposito L., Vitagliano L., Mazzarella L., Recent advances in atomic resolution protein crystallography. Protein and Peptide Letters 2002 9 2 95 105 2-s2.0-0036527061 (Pubitemid 34432245)
    • (2002) Protein and Peptide Letters , vol.9 , Issue.2 , pp. 95-105
    • Esposito, L.1    Vitagliano, L.2    Mazzarella, L.3
  • 7
    • 80052850167 scopus 로고    scopus 로고
    • Peptide bond distortions from planarity: New insights from quantum mechanical calculations and peptide/protein crystal structures
    • 2-s2.0-80052850167 10.1371/journal.pone.0024533 e24533
    • Improta R., Vitagliano L., Esposito L., Peptide bond distortions from planarity: new insights from quantum mechanical calculations and peptide/protein crystal structures. PLoS ONE 2011 6 9 2-s2.0-80052850167 10.1371/journal.pone. 0024533 e24533
    • (2011) PLoS ONE , vol.6 , Issue.9
    • Improta, R.1    Vitagliano, L.2    Esposito, L.3
  • 8
    • 40449110032 scopus 로고    scopus 로고
    • A forward-looking suggestion for resolving the stereochemical restraints debate: Ideal geometry functions
    • DOI 10.1107/S0907444908002333, PII S0907444908002333
    • Karplus P. A., Shapovalov M. V., Dunbrack R. L. Jr., Berkholz D. S., A forward-looking suggestion for resolving the stereochemical restraints debate: ideal geometry functions. Acta Crystallographica D 2008 64 3 335 336 2-s2.0-40449110032 10.1107/S0907444908002333 (Pubitemid 351348060)
    • (2008) Acta Crystallographica Section D: Biological Crystallography , vol.64 , Issue.3 , pp. 335-336
    • Karplus, P.A.1    Shapovalov, M.V.2    Dunbrack, R.L.3    Berkholz, D.S.4
  • 9
    • 75549085702 scopus 로고    scopus 로고
    • Protein geometry database: A flexible engine to explore backbone conformations and their relationships to covalent geometry
    • 2-s2.0-75549085702 10.1093/nar/gkp1013
    • Berkholz D. S., Krenesky P. B., Davidson J. R., Karplus P. A., Protein geometry database: a flexible engine to explore backbone conformations and their relationships to covalent geometry. Nucleic Acids Research 2010 38 1 D320 D325 2-s2.0-75549085702 10.1093/nar/gkp1013
    • (2010) Nucleic Acids Research , vol.38 , Issue.1
    • Berkholz, D.S.1    Krenesky, P.B.2    Davidson, J.R.3    Karplus, P.A.4
  • 10
    • 70349758444 scopus 로고    scopus 로고
    • Conformation dependence of backbone geometry in proteins
    • 2-s2.0-70349758444 10.1016/j.str.2009.08.012
    • Berkholz D. S., Shapovalov M. V., Dunbrack R. L. Jr., Karplus P. A., Conformation dependence of backbone geometry in proteins. Structure 2009 17 10 1316 1325 2-s2.0-70349758444 10.1016/j.str.2009.08.012
    • (2009) Structure , vol.17 , Issue.10 , pp. 1316-1325
    • Berkholz, D.S.1    Shapovalov, M.V.2    Dunbrack Jr., R.L.3    Karplus, P.A.4
  • 12
    • 34247534257 scopus 로고    scopus 로고
    • Stereochemical restraints revisited: How accurate are refinement targets and how much should protein structures be allowed to deviate from them?
    • DOI 10.1107/S090744490700978X, PII S090744490700978X, wd5076
    • Jaskolski M., Gilski M., Dauter Z., Wlodawer A., Stereochemical restraints revisited: how accurate are refinement targets and how much should protein structures be allowed to deviate from them? Acta Crystallographica D 2007 63 5 611 620 2-s2.0-34247534257 10.1107/S090744490700978X wd5076 (Pubitemid 46661532)
    • (2007) Acta Crystallographica Section D: Biological Crystallography , vol.63 , Issue.5 , pp. 611-620
    • Jaskolski, M.1    Gilski, M.2    Dauter, Z.3    Wlodawer, A.4
  • 14
    • 34748886126 scopus 로고    scopus 로고
    • Comment on Stereochemical restraints revisited: How accurate are refinement targets and how much should protein structures be allowed to deviate from them? By Jaskolski, Gilski, Dauter & Wlodawer (2007)
    • DOI 10.1107/S0907444907041406, PII S0907444907041406
    • Stec B., Comment on stereochemical restraints revisited: how accurate are refinement targets and how much should protein structures be allowed to deviate from them? By Jaskolski, Gilski, Dauter & Wlodawer (2007). Acta Crystallographica D 2007 63 10 1113 1114 2-s2.0-34748886126 10.1107/ S0907444907041406 (Pubitemid 47480525)
    • (2007) Acta Crystallographica Section D: Biological Crystallography , vol.63 , Issue.10 , pp. 1113-1114
    • Stec, B.1
  • 15
    • 36849061816 scopus 로고    scopus 로고
    • Experimental determination of optimal root-mean-square deviations of macromolecular bond lengths and angles from their restrained ideal values
    • DOI 10.1107/S0907444907050196, PII S0907444907050196
    • Tickle I. J., Experimental determination of optimal root-mean-square deviations of macromolecular bond lengths and angles from their restrained ideal values. Acta Crystallographica D 2007 63 12 1274 1281 2-s2.0-36849061816 10.1107/S0907444907050196 (Pubitemid 350222119)
    • (2007) Acta Crystallographica Section D: Biological Crystallography , vol.63 , Issue.12 , pp. 1274-1281
    • Tickle, I.J.1
  • 16
    • 70349777585 scopus 로고    scopus 로고
    • Proteins do not have strong spines after all
    • 2-s2.0-70349777585 10.1016/j.str.2009.09.002
    • Dauter Z., Wlodawer A., Proteins do not have strong spines after all. Structure 2009 17 10 1278 1279 2-s2.0-70349777585 10.1016/j.str.2009.09.002
    • (2009) Structure , vol.17 , Issue.10 , pp. 1278-1279
    • Dauter, Z.1    Wlodawer, A.2
  • 17
    • 0034829669 scopus 로고    scopus 로고
    • Structure and conformational behavior of biopolymers by density functional calculations employing periodic boundary conditions. I. The case of polyglycine, polyalanine, and poly-α-aminoisobutyric acid in vacuo
    • DOI 10.1021/ja003680e
    • Improta R., Barone V., Kudin K. N., Scuseria G. E., Structure and conformational behavior of biopolymers by density functional calculations employing periodic boundary conditions. I. The case of polyglycine, polyalanine, and poly- α-aminoisobutyric acid in vacuo. Journal of the American Chemical Society 2001 123 14 3311 3322 2-s2.0-0034829669 10.1021/ja003680e (Pubitemid 32884620)
    • (2001) Journal of the American Chemical Society , vol.123 , Issue.14 , pp. 3311-3322
    • Improta, R.1    Barone, V.2    Kudin, K.N.3    Scuseria, G.E.4
  • 18
    • 78649817914 scopus 로고    scopus 로고
    • On the complexity of Engh and Huber refinement restraints: The angle τ as example
    • 2-s2.0-78649817914 10.1107/S0907444910040928
    • Touw W. G., Vriend G., On the complexity of Engh and Huber refinement restraints: the angle τ as example. Acta Crystallographica D 2010 66 12 1341 1350 2-s2.0-78649817914 10.1107/S0907444910040928
    • (2010) Acta Crystallographica D , vol.66 , Issue.12 , pp. 1341-1350
    • Touw, W.G.1    Vriend, G.2
  • 19
    • 0033773831 scopus 로고    scopus 로고
    • Pyramidalization of backbone carbonyl carbon atoms in proteins
    • 2-s2.0-0033773831
    • Esposito L., Vitagliano L., Zagari A., Mazzarella L., Pyramidalization of backbone carbonyl carbon atoms in proteins. Protein Science 2000 9 10 2038 2042 2-s2.0-0033773831
    • (2000) Protein Science , vol.9 , Issue.10 , pp. 2038-2042
    • Esposito, L.1    Vitagliano, L.2    Zagari, A.3    Mazzarella, L.4
  • 20
    • 63449103818 scopus 로고    scopus 로고
    • Role of side chains in collagen triple helix stabilization and partner recognition
    • 2-s2.0-63449103818 10.1002/psc.1082
    • Berisio R., de Simone A., Ruggiero A., Improta R., Vitagliano L., Role of side chains in collagen triple helix stabilization and partner recognition. Journal of Peptide Science 2009 15 3 131 140 2-s2.0-63449103818 10.1002/psc.1082
    • (2009) Journal of Peptide Science , vol.15 , Issue.3 , pp. 131-140
    • Berisio, R.1    De Simone, A.2    Ruggiero, A.3    Improta, R.4    Vitagliano, L.5
  • 21
    • 67650726873 scopus 로고    scopus 로고
    • Collagen structure and stability
    • 2-s2.0-67650726873 10.1146/annurev.biochem.77.032207.120833
    • Shoulders M. D., Raines R. T., Collagen structure and stability. Annual Review of Biochemistry 2009 78 929 958 2-s2.0-67650726873 10.1146/annurev. biochem.77.032207.120833
    • (2009) Annual Review of Biochemistry , vol.78 , pp. 929-958
    • Shoulders, M.D.1    Raines, R.T.2
  • 22
    • 56349098272 scopus 로고    scopus 로고
    • Revisiting the molecular structure of collagen
    • 2-s2.0-56349098272 10.1080/03008200802325110
    • Okuyama K., Revisiting the molecular structure of collagen. Connective Tissue Research 2008 49 5 299 310 2-s2.0-56349098272 10.1080/03008200802325110
    • (2008) Connective Tissue Research , vol.49 , Issue.5 , pp. 299-310
    • Okuyama, K.1
  • 23
    • 20444440728 scopus 로고    scopus 로고
    • Structure of the cross-β spine of amyloid-like fibrils
    • DOI 10.1038/nature03680
    • Nelson R., Sawaya M. R., Balbirnie M., Madsen A. Ø., Riekel C., Grothe R., Eisenberg D., Structure of the cross- β spine of amyloid-like fibrils. Nature 2005 435 7043 773 778 2-s2.0-20444440728 10.1038/nature03680 (Pubitemid 40839722)
    • (2005) Nature , vol.435 , Issue.7043 , pp. 773-778
    • Nelson, R.1    Sawaya, M.R.2    Balbirnie, M.3    Madsen, A.O.4    Riekel, C.5    Grothe, R.6    Eisenberg, D.7
  • 25
    • 17444415358 scopus 로고    scopus 로고
    • Molecular structure of the collagen triple helix
    • DOI 10.1016/S0065-3233(05)70009-7, Fibrous Proteins Coiled-Coils, Collagen and Elastomers
    • Brodsky B., Persikov A. V., Molecular structure of the collagen triple helix. Advances in Protein Chemistry 2005 70 301 339 2-s2.0-17444415358 10.1016/S0065-3233(05)70009-7 (Pubitemid 40544786)
    • (2005) Advances in Protein Chemistry , vol.70 , pp. 301-339
    • Brodsky, B.1    Persikov, A.V.2
  • 26
    • 33845275819 scopus 로고    scopus 로고
    • Estimation of membrane proteins in the human proteome
    • Ahram M., Litou Z. I., Fang R., Al-Tawallbeh G., Estimation of membrane proteins in the human proteome. In Silico Biology 2006 6 5 379 386 2-s2.0-33845275819 (Pubitemid 44857635)
    • (2006) Silico Biology , vol.6 , Issue.5 , pp. 379-386
    • Ahram, M.1    Litou, Z.I.2    Fang, R.3    Al-Tawallbeh, G.4
  • 28
    • 33846036096 scopus 로고    scopus 로고
    • The worldwide Protein Data Bank (wwPDB): Ensuring a single, uniform archive of PDB data
    • DOI 10.1093/nar/gkl971
    • Berman H., Henrick K., Nakamura H., Markley J. L., The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Research 2007 35 1 D301 D303 2-s2.0-33846036096 10.1093/nar/gkl971 (Pubitemid 46056219)
    • (2007) Nucleic Acids Research , vol.35 , Issue.SUPPL. 1
    • Berman, H.1    Henrick, K.2    Nakamura, H.3    Markley, J.L.4
  • 29
    • 84874677954 scopus 로고    scopus 로고
    • PDBTM: Protein data bank of transmembrane proteins after 8 years
    • Kozma D., Simon I., Tusnady G. E., PDBTM: protein data bank of transmembrane proteins after 8 years. Nucleic Acids Research 2013 41 D524 D529
    • (2013) Nucleic Acids Research , vol.41
    • Kozma, D.1    Simon, I.2    Tusnady, G.E.3
  • 30
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • 2-s2.0-0020997912
    • Kabsch W., Sander C., Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983 22 12 2577 2637 2-s2.0-0020997912
    • (1983) Biopolymers , vol.22 , Issue.12 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 31
    • 84876807065 scopus 로고    scopus 로고
    • Crystal structure of the collagen model peptide (Pro-Pro-Gly)4 -Hyp-Asp-Gly-(Pro-Pro-Gly)4 at 1.0 A resolution
    • Okuyama K., Kawaguchi T., Shimura M., Noguchi K., Mizuno K., Bachinger H. P., Crystal structure of the collagen model peptide (Pro-Pro-Gly)4 -Hyp-Asp-Gly-(Pro-Pro-Gly)4 at 1.0 A resolution. Biopolymers 2013 99 436 447
    • (2013) Biopolymers , vol.99 , pp. 436-447
    • Okuyama, K.1    Kawaguchi, T.2    Shimura, M.3    Noguchi, K.4    Mizuno, K.5    Bachinger, H.P.6
  • 32
    • 79959746704 scopus 로고    scopus 로고
    • Stabilization of triple-helical structures of collagen peptides containing a Hyp-Thr-Gly, Hyp-Val-Gly, or Hyp-Ser-Gly sequence
    • 2-s2.0-79959746704 10.1002/bip.21625
    • Okuyama K., Miyama K., Morimoto T., Masakiyo K., Mizuno K., Bächinger H. P., Stabilization of triple-helical structures of collagen peptides containing a Hyp-Thr-Gly, Hyp-Val-Gly, or Hyp-Ser-Gly sequence. Biopolymers 2011 95 9 628 640 2-s2.0-79959746704 10.1002/bip.21625
    • (2011) Biopolymers , vol.95 , Issue.9 , pp. 628-640
    • Okuyama, K.1    Miyama, K.2    Morimoto, T.3    Masakiyo, K.4    Mizuno, K.5    Bächinger, H.P.6
  • 33
    • 33645742624 scopus 로고    scopus 로고
    • Revision of collagen molecular structure
    • 2-s2.0-33645742624 10.1002/bip.20381
    • Okuyama K., Xu X., Iguchi M., Noguchi K., Revision of collagen molecular structure. Biopolymers 2006 84 2 181 191 2-s2.0-33645742624 10.1002/bip.20381
    • (2006) Biopolymers , vol.84 , Issue.2 , pp. 181-191
    • Okuyama, K.1    Xu, X.2    Iguchi, M.3    Noguchi, K.4
  • 34
    • 84874856515 scopus 로고    scopus 로고
    • Polyproline and triple helix motifs in host-pathogen recognition
    • Berisio R., Vitagliano L., Polyproline and triple helix motifs in host-pathogen recognition. Current Protein & Peptide Science 2012 13 855 865
    • (2012) Current Protein & Peptide Science , vol.13 , pp. 855-865
    • Berisio, R.1    Vitagliano, L.2
  • 35
    • 79960949121 scopus 로고    scopus 로고
    • A conformation-dependent stereochemical library improves crystallographic refinement even at atomic resolution
    • 2-s2.0-79960949121 10.1107/S090744491102292X
    • Tronrud D. E., Karplus P. A., A conformation-dependent stereochemical library improves crystallographic refinement even at atomic resolution. Acta Crystallographica D 2011 67 8 699 706 2-s2.0-79960949121 10.1107/ S090744491102292X
    • (2011) Acta Crystallographica D , vol.67 , Issue.8 , pp. 699-706
    • Tronrud, D.E.1    Karplus, P.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.