Peptide bond planarity constrains hydrogen bond geometry and influences secondary structure conformations

Alabugin, 2011, Hyperconjugation, Wiley Interdiscip. Rev. Comput. Mol. Sci., 1, 109, 10.1002/wcms.6 Allen, 2002, The Cambridge Structural Database: a quarter of a million crystal structures and rising, Acta Crystallogr. Sect. B Struct. Sci., 58, 380, 10.1107/S0108768102003890 Arunan, 2011, Definition of the hydrogen bond (IUPAC Recommendations 2011), Pure Appl. Chem., 83, 10.1351/PAC-REC-10-01-02 Arunan, 2011, Defining the hydrogen bond: an account (IUPAC Technical Report), Pure Appl. Chem., 83, 10.1351/PAC-REP-10-01-01 Baker, 1984, Hydrogen bonding in globular proteins, Prog. Biophys. Mol. Biol., 44, 97, 10.1016/0079-6107(84)90007-5 Ben-Naim, 1991, The role of hydrogen bonds in protein folding and protein association, J. Phys. Chem., 95, 1437, 10.1021/j100156a074 Berman, 2000, The protein data bank, Nucleic Acids Res., 28, 235, 10.1093/nar/28.1.235 Bordo, 1994, The role of side-chain hydrogen bonds in the formation and stabilization of secondary structure in soluble proteins, J. Mol. Biol., 243, 504, 10.1006/jmbi.1994.1676 Buck, 2001, Hydrogen bond energetics: a simulation and statistical analysis of N-methyl acetamide (NMA), water, and human lysozyme, J. Phys. Chem. B, 105, 11000, 10.1021/jp011042s Byrne, 1995, Energetic contribution of side chain hydrogen bonding to the stability of staphylococcal nuclease, Biochemistry, 34, 13949, 10.1021/bi00042a029 Campos, 2005, A double-deletion method to quantifying incremental binding energies in proteins from experiment: example of a destabilizing hydrogen bonding pair, Biophys. J., 88, 1311, 10.1529/biophysj.104.050203 Cao, 2014, An energetic scale for equilibrium H/D fractionation factors illuminates hydrogen bond free energies in proteins, Protein Sci., 23, 566, 10.1002/pro.2435 Chakravarty, 1999, Residue depth: a novel parameter for the analysis of protein structure and stability, Structure, 7, 723, 10.1016/S0969-2126(99)80097-5 Chatterjee, 2009, Expanding the peptide β -turn in α γ hybrid sequences: 12 atom hydrogen bonded helical and hairpin turns, J. Am. Chem. Soc., 131, 5956, 10.1021/ja900618h Connelly, 1994, Enthalpy of hydrogen bond formation in a protein-ligand binding reaction, Proc. Natl. Acad. Sci. Unit. States Am., 91, 1964, 10.1073/pnas.91.5.1964 Cordier, 2002, Temperature-dependence of protein hydrogen bond properties as studied by high-resolution NMR, J. Mol. Biol., 317, 739, 10.1006/jmbi.2002.5446 Cordier, 1999, Observation of through-hydrogen-bond 2hJHC' in a perdeuterated protein, J. Magn. Reson., 140, 510, 10.1006/jmre.1999.1899 Deechongkit, 2004, Context-dependent contributions of backbone hydrogen bonding to β-sheet folding energetics, Nature, 430, 101, 10.1038/nature02611 Eberhardt, 1994, Amide-amide and amide-water hydrogen bonds: implications for protein folding and stability, J. Am. Chem. Soc., 116, 2149, 10.1021/ja00084a067 Eswar, 1999, Secondary structures without backbone: an analysis of backbone mimicry by polar side chains in protein structures, Protein Eng., 12, 447, 10.1093/protein/12.6.447 Eswar, 2000, Deterministic features of side-chain main-chain hydrogen bonds in globular protein structures, Protein Eng., 13, 227, 10.1093/protein/13.4.227 Fabiola, 2002, An improved hydrogen bond potential: impact on medium resolution protein structures, Protein Sci., 11, 1415, 10.1110/ps.4890102 Fersht, 1987, The hydrogen bond in molecular recognition, Trends Biochem. Sci., 12, 301, 10.1016/0968-0004(87)90146-0 Graulis, 2009, Crystallography Open Database - an open-access collection of crystal structures, J. Appl. Crystallogr., 42, 726, 10.1107/S0021889809016690 Gražulis, 2012, Crystallography Open Database (COD): an open-access collection of crystal structures and platform for world-wide collaboration, Nucleic Acids Res., 40, D420, 10.1093/nar/gkr900 Grzybowski, 2000, Development of a knowledge-based potential for crystals of small organic molecules: calculation of energy surfaces for C=0···H−N hydrogen bonds, J. Phys. Chem. B, 104, 7293, 10.1021/jp000644t Habermann, 1996, Energetics of hydrogen bonding in proteins: a model compound study, Protein Sci., 5, 1229, 10.1002/pro.5560050702 Honig, 1999, Protein folding: from the levinthal paradox to structure prediction, J. Mol. Biol., 293, 283, 10.1006/jmbi.1999.3006 Honig, 1995, Free energy balance in protein folding, Adv. Protein Chem., 46, 27, 10.1016/S0065-3233(08)60331-9 Ippolito, 1990, Hydrogen bond stereochemistry in protein structure and function, J. Mol. Biol., 215, 457, 10.1016/S0022-2836(05)80364-X Isaacs, 1999, Covalency of the hydrogen bond in ice: a direct x-ray measurement, Phys. Rev. Lett., 82, 600, 10.1103/PhysRevLett.82.600 Kabsch, 1983, Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features, Biopolymers, 22, 2577, 10.1002/bip.360221211 Kortemme, 2003, An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes, J. Mol. Biol., 326, 1239, 10.1016/S0022-2836(03)00021-4 Kurochkina, 1998, Heterogeneity of packing: structural approach, Protein Sci., 7, 897, 10.1002/pro.5560070407 Lazaridis, 1995, Enthalpic contribution to protein stability: insights from atom-based calculations and statistical mechanics, Adv. Protein Chem., 47, 231, 10.1016/S0065-3233(08)60547-1 Lommerse, 1997, Hydrogen bonding of carbonyl, ether, and ester oxygen atoms with alkanol hydroxyl groups, J. Comput. Chem., 18, 757, 10.1002/(SICI)1096-987X(19970430)18:6<757::AID-JCC3>3.0.CO;2-R McDonald, 1994, Satisfying hydrogen bonding potential in proteins, J. Mol. Biol., 238, 777, 10.1006/jmbi.1994.1334 Miller, 2007, Modeling competitive interactions in proteins: vibrational spectroscopy of M+(n-methylacetamide)1(H2O)n=0-3, M = Na and K, in the 3 mm region, J. Phys. Chem. A, 111, 12409, 10.1021/jp073521i Morozov, 2004, Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations, Proc. Natl. Acad. Sci. Unit. States Am., 101, 6946, 10.1073/pnas.0307578101 Myers, 1996, Hydrogen bonding stabilizes globular proteins, Biophys. J., 71, 2033, 10.1016/S0006-3495(96)79401-8 Nick Pace, 2014, Forces stabilizing proteins, FEBS Lett., 588, 2177, 10.1016/j.febslet.2014.05.006 Nisius, 2012, Key stabilizing elements of protein structure identified through pressure and temperature perturbation of its hydrogen bond network, Nat. Chem., 4, 711, 10.1038/nchem.1396 Pace, 2009, Energetics of protein hydrogen bonds, Nat. Struct. Mol. Biol., 16, 681, 10.1038/nsmb0709-681 Pace, 2014, Contribution of hydrogen bonds to protein stability, Protein Sci., 23, 652, 10.1002/pro.2449 Raghavendra, 2006, Ab initio and AIM theoretical analysis of hydrogen-bond radius of HD (D = F, Cl, Br, CN, HO, HS and CCH) donors and some acceptors, Phys. Chem. Chem. Phys., 8, 5276, 10.1039/b611033a Richards, 1988, Identification of structural motifs from protein coordinate data: secondary structure and first-level supersecondary structure, Proteins Struct. Funct. Bioinforma., 3, 71, 10.1002/prot.340030202 Rose, 2006, A backbone-based theory of protein folding, Proc. Natl. Acad. Sci. Unit. States Am., 103, 16623, 10.1073/pnas.0606843103 Šali, 1993, Comparative protein modelling by satisfaction of spatial restraints, J. Mol. Biol., 234, 779, 10.1006/jmbi.1993.1626 Schell, 2006, Hydrogen bonding increases packing density in the protein interior, Proteins Struct. Funct. Genet., 63, 278, 10.1002/prot.20826 Schmidt, 1993, General atomic and molecular electronic structure system, J. Comput. Chem., 14, 1347, 10.1002/jcc.540141112 Sheu, 2003, Energetics of hydrogen bonds in peptides, Proc. Natl. Acad. Sci. Unit. States Am., 100, 12683, 10.1073/pnas.2133366100 Shirley, 1992, Contribution of hydrogen bonding to the conformational stability of ribonuclease, Biochemistry, 31, 725, 10.1021/bi00118a013 Sticke, 1992, Hydrogen bonding in globular proteins, J. Mol. Biol., 226, 1143, 10.1016/0022-2836(92)91058-W Tan, 2011, DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins, Nucleic Acids Res., 39, 10.1093/nar/gkr356 Tan, 2013, Depth: a web server to compute depth, cavity sizes, detect potential small-molecule ligand-binding cavities and predict the pKa of ionizable residues in proteins, Nucleic Acids Res., 41, 10.1093/nar/gkt503 Taylor, 1984, Hydrogen-bond geometry in organic crystals†, Acc. Chem. Res., 17, 320, 10.1021/ar00105a004 Taylor, 1983, Geometry of the N-H ⃛O=C hydrogen bond. 1. Lone-pair directionality, J. Am. Chem. Soc., 105, 5761, 10.1021/ja00356a010 Thurlkill, 2006, Hydrogen bonding markedly reduces the pK of buried carboxyl groups in proteins, J. Mol. Biol., 362, 594, 10.1016/j.jmb.2006.07.056 Torshin, 2002, Geometric criteria of hydrogen bonds in proteins and identification of 'bifurcated’ hydrogen bonds, Protein Eng. Des. Sel., 15, 359, 10.1093/protein/15.5.359 Van Gunsteren, 1996