Aggregation of capped hexaglycine strands into hydrogen-bonding motifs representative of pleated and rippled β-sheets, collagen, and polyglycine I and II crystal structures. A density functional theory study.
We compare the energies and enthalpies of inter-action of three- and seven-stranded capped polyglycine aggregates in both the pleated and rippled antiparallel and parallel β-sheet structures as well as the collagenic (three-strand) or polyglycine II-like (seven-strand) forms using density functional theory at the B3LYP/D95(d,p) level. We present the overall interaction energies as broken down into pure H-bonding between the strands at the geometries they assume in the aggregates and the distortion energies required to achieve those geometries starting from the fully relaxed single strands. While the antiparallel sheets represent the most stable structures for both the three- and seven-strand structures, the pure H-bonding interactions are the smallest for these structures. The overall interaction energies are dominated by the energy required to distort the relaxed polyglycine strands rather than the H-bonding energies. The antiparallel β-sheet constrained to C(s) symmetry has a lower enthalpy, but higher energy, of interaction than the fully optimized structure.
Department of Chemistry, Hunter College and the Graduate School, City University of New York, 695 Park Avenue, New York, New York 10065, USA.
Joshua A
JA
Plumley
Midas I-Hsien
MI
Tsai
J J
JJ
Dannenberg
D003094:Collagen / Q000737:chemistry*; D018360:Crystallography, X-Ray; D006860:Hydrogen Bonding; D008962:Models, Theoretical; D009842:Oligopeptides / Q000737:chemistry*; D010455:Peptides / Q000737:chemistry*; D017433:Protein Structure, Secondary; D013816:Thermodynamics
D009842:Oligopeptides; D010455:Peptides; C011080:polyglycine; D003094:Collagen
Org Lett. 2007 May 10;9(10):1851-4
17417862
J Phys Chem B. 2008 Feb 14;112(6):1765-9
18211062
J Comput Chem. 2008 Jul 15;29(9):1374-86
18196503
J Phys Chem B. 2008 Apr 24;112(16):5199-208
18386875
Phys Rev B Condens Matter. 1988 Jan 15;37(2):785-789
9944570
J Am Chem Soc. 2004 Nov 3;126(43):14198-205
15506786
J Am Chem Soc. 2001 Apr 11;123(14):3311-22
11457067
J Mol Biol. 1983 Jun 15;167(1):223-5
6864802
J Am Chem Soc. 2001 May 9;123(18):4348-9
11457207
J Am Chem Soc. 2002 Feb 27;124(8):1570-1
11853419
J Am Chem Soc. 2006 Jun 28;128(25):8100-1
16787050
Nature. 1949 May 7;163(4149):722
18126651
J Mol Biol. 1974 Aug 5;87(2):169-80
4427364
J Mol Biol. 1961 Oct;3:483-506
14491907
Acta Crystallogr D Biol Crystallogr. 1999 Feb;55(Pt 2):436-42
10089352
Nature. 1955 Oct 22;176(4486):780-1
13265825
J Mol Biol. 1974 Aug 5;87(2):181-91
4427365
Proc Natl Acad Sci U S A. 1953 Apr;39(4):253-6
16589257
J Comput Chem. 2011 Jun;32(8):1519-27
21328398
J Am Chem Soc. 2005 Oct 19;127(41):14130-1
16218576
J Am Chem Soc. 2010 Feb 17;132(6):1758-9
20088582