NCAD, a database integrating the intrinsic conformational preferences of non-coded amino acids.
Peptides and proteins find an ever-increasing number of applications in the biomedical and materials engineering fields. The use of non-proteinogenic amino acids endowed with diverse physicochemical and structural features opens the possibility to design proteins and peptides with novel properties and functions. Moreover, non-proteinogenic residues are particularly useful to control the three-dimensional arrangement of peptidic chains, which is a crucial issue for most applications. However, information regarding such amino acids--also called non-coded, non-canonical, or non-standard--is usually scattered among publications specialized in quite diverse fields as well as in patents. Making all these data useful to the scientific community requires new tools and a framework for their assembly and coherent organization. We have successfully compiled, organized, and built a database (NCAD, Non-Coded Amino acids Database) containing information about the intrinsic conformational preferences of non-proteinogenic residues determined by quantum mechanical calculations, as well as bibliographic information about their synthesis, physical and spectroscopic characterization, conformational propensities established experimentally, and applications. The architecture of the database is presented in this work together with the first family of non-coded residues included, namely, alpha-tetrasubstituted alpha-amino acids. Furthermore, the NCAD usefulness is demonstrated through a test-case application example.
Revilla-López
Guillem
G
Departament d'Enginyeria Química, E. T. S. d'Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain.
Torras
Juan
J
Curcó
David
D
Casanovas
Jordi
J
Calaza
M Isabel
MI
Zanuy
David
D
Jiménez
Ana I
AI
Cativiela
Carlos
C
Nussinov
Ruth
R
Grodzinski
Piotr
P
Alemán
Carlos
C
D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry*; D016208:Databases, Factual; D030562:Databases, Protein
D000596:Amino Acids
Proc Natl Acad Sci U S A. 2006 Jun 27;103(26):9785-9
16785423
Acc Chem Res. 2008 Oct;41(10):1399-408
18590282
Chem Rev. 2001 Oct;101(10):3131-52
11710065
J Am Chem Soc. 2003 Dec 3;125(48):14662-3
14640614
J Phys Chem B. 2007 Mar 29;111(12):3236-42
17388467
Biochem Biophys Res Commun. 1978 Mar 30;81(2):602-9
666773
Peptides. 2009 Dec;30(12):2432-79
19793543
Nat Chem Biol. 2007 Dec;3(12):769-72
17965709
Proc Natl Acad Sci U S A. 2006 Mar 21;103(12):4356-61
16537388
Biopolymers. 2004;76(3):206-43
15148683
Curr Opin Chem Biol. 2004 Dec;8(6):604-9
15556403
Angew Chem Int Ed Engl. 2005 Sep 5;44(35):5710-3
16080230
Curr Med Chem. 2009;16(33):4399-418
19835565
J Nat Prod. 1996 Dec;59(12):1205-11
8988607
Chemistry. 2005 Dec 16;12(1):251-60
16281320
J Org Chem. 2007 Mar 16;72(6):2174-81
17291048
Rapid Commun Mass Spectrom. 2005;19(1):1-8
15568184
Nat Methods. 2005 Mar;2(3):201-6
15782189
Soft Matter. 2007 Mar 20;3(4):394-408
32900058
J Pept Sci. 2002 Jun;8(6):253-66
12093002
Nature. 1975 Dec 18;258(5536):577-80
1207728
J Org Chem. 2009 Mar 20;74(6):2403-12
19236034
Adv Protein Chem. 2001;56:13-75
11329852
J Org Chem. 2009 Oct 16;74(20):7834-43
19772338
J Am Chem Soc. 2009 Sep 9;131(35):12497-515
19689159
J Am Chem Soc. 2006 Jan 18;128(2):388-9
16402807
Nat Prod Rep. 2003 Jun;20(3):275-87
12828367
Tetrahedron Asymmetry. 2009 Jan 30;20(1):1-63
20300486
Small. 2007 Apr;3(4):558-62
17323399
Biochemistry. 2003 Mar 4;42(8):2441-8
12600211
Trends Biochem Sci. 1995 Sep;20(9):374
7482707
Nucleic Acids Res. 2000 Jan 1;28(1):235-42
10592235
J Org Chem. 2008 May 2;73(9):3418-27
18351745
Acc Chem Res. 2008 Oct;41(10):1366-75
18578513
J Phys Chem B. 2006 Oct 26;110(42):21264-71
17048955
Acta Crystallogr B. 2002 Jun;58(Pt 3 Pt 1):380-8
12037359
Chem Rev. 2004 Dec;104(12):5823-46
15584690
J Comput Chem. 2005 Dec;26(16):1781-802
16222654
Chem Soc Rev. 2009 Jul;38(7):2093-116
19551183
Biopolymers. 2001;60(6):396-419
12209474
J Chem Inf Model. 2008 Feb;48(2):333-43
18201062
Curr Med Chem. 2004 Nov;11(21):2785-98
15544476
Proc Natl Acad Sci U S A. 1986 May;83(10):3272-6
3458181
Angew Chem Int Ed Engl. 2004 Dec 17;44(1):34-66
15599909
Proteins. 1999 Mar 1;34(4):472-83
10081960
Acta Crystallogr D Biol Crystallogr. 1998 Nov 1;54(Pt 6 Pt 1):1078-84
10089483
J Am Chem Soc. 2005 Feb 23;127(7):2036-7
15713068
Curr Opin Struct Biol. 1999 Aug;9(4):530-5
10449369
Science. 1993 Sep 3;261(5126):1303-5
7689747
J Phys Chem B. 2006 Mar 23;110(11):5762-6
16539522
Biopolymers. 2006 Apr 5;81(5):339-49
16345001
Science. 2001 Apr 20;292(5516):498-500
11313494
Proc Natl Acad Sci U S A. 1998 Apr 14;95(8):4303-8
9539732
Biochem Biophys Res Commun. 1976 May 23;76(2):224-31
1027428
J Am Chem Soc. 2008 Jul 23;130(29):9268-81
18576636
J Chem Inf Model. 2009 Jul;49(7):1623-9
19548653
Proc Natl Acad Sci U S A. 1987 Oct;84(19):6611-5
3477791
Eur J Biochem. 1979 Jun;97(1):43-57
38962
Mol Biosyst. 2010 Jan;6(1):65-80
20024068
Science. 2001 Nov 23;294(5547):1684-8
11721046
Org Biomol Chem. 2003 Jun 7;1(11):1980-8
12945783
Adv Drug Deliv Rev. 2004 Sep 22;56(11):1537-63
15350288
J Am Chem Soc. 2009 Sep 16;131(36):12921-3
19702307
J Am Chem Soc. 2009 Nov 25;131(46):16779-89
19886604
Angew Chem Int Ed Engl. 2008;47(7):1202-23
18076006
Chem Biodivers. 2008 Sep;5(9):1817-43
18816513
Biophys J. 2004 Mar;86(3):1587-600
14990485
J Org Chem. 2008 Jan 18;73(2):644-51
18081347
J Org Chem. 2008 Jun 6;73(11):4205-11
18465898
J Am Chem Soc. 2005 Feb 2;127(4):1193-200
15669858
Proc Natl Acad Sci U S A. 2008 Jun 24;105(25):8513-8
18559857
Org Lett. 2006 Dec 21;8(26):6091-4
17165937
J Org Chem. 2003 Sep 5;68(18):7088-91
12946154
Proc Natl Acad Sci U S A. 2002 Jan 8;99(1):19-24
11752401
Curr Med Chem. 2004 Nov;11(21):2799-822
15544477
Org Lett. 2002 Aug 22;4(17):2865-8
12182575
Biomacromolecules. 2000 Spring;1(1):118-25
11709833
Proteins. 2002 Feb 1;46(2):225-34
11807951
J Pept Sci. 2004 May;10(5):274-84
15160839
J Am Chem Soc. 2003 Aug 27;125(34):10150-1
12926919
Tetrahedron. 2009 Jan 3;65(1):17-49
20871799
Biopolymers. 1992 Dec;32(12):1755-64
1472657
Nat Neurosci. 2007 Aug;10(8):1063-72
17603477
Annu Rev Biochem. 2004;73:147-76
15189139
Curr Med Chem. 2002 May;9(9):963-78
11966456
Acc Chem Res. 2008 Oct;41(10):1331-42
18636716