Rapid Prediction of the Hydrogen Bond Cooperativity in<i>N</i>‐methylacetamide Chains

Jiang, Xiaonan; Wang, Chang-Sheng

doi:10.1002/cphc.200900591

Cited by 30 publications

(29 citation statements)

References 73 publications

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“…One must have both accurate estimates of shifts of individual conformers and of relative populations in order to obtain a useful estimate of the average resonance position. The QM/MM calculated 1 H chemical shifts are systematically underestimated by ~1.4 ppm, a pattern that has been seen in studies of folded proteins as well 32,37 . The empirical SHIFTX2 models are trained to give average shifts from a single conformation, and thus have a bias towards understating conformational variability (Figure 4b).…”

Section: Resultssupporting

confidence: 52%

Dynamic Water-Mediated Hydrogen Bonding in a Collagen Model Peptide

Case

Baum

2015

Biochemistry

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In the canonical (G-X-Y)n sequence of the fibrillar collagen triple helix, stabilizing direct inter-chain hydrogen bonding connects neighboring chains. Mutations at G can disrupt these interactions and are linked to connective tissue diseases. Here we integrate computational approaches with NMR to obtain a dynamic view of hydrogen bonding distributions in the (POG)4-(POA)-(POG)5 peptide, showing that the solution conformation, dynamics and hydrogen bonding deviate from the reported x-ray crystal structure in many aspects. The simulations and NMR data provide clear evidence for inequivalent environments in the three chains. MD simulations indicate direct inter-chain hydrogen bonds in the leading chain, water-bridges in the middle chain, and non-bridging waters in the trailing chain at the G→A substitution site. Theoretical calculations of NMR chemical shifts using a quantum fragmentation procedure can account for the unusual downfield NMR chemical shifts at the substitution sites and are used to assign the resonances to the individual chains. The NMR and MD data highlight the sensitivity of amide shifts to changes in the acceptor group from peptide carbonyls to water. The results are used to interpret solution NMR data for a variety of glycine substitutions and other sequence triplet interruptions, to provide new connections between collagen sequences, their associated structures, dynamical behavior and ability to recognize collagen receptors.

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Section: Resultssupporting

confidence: 52%

Dynamic Water-Mediated Hydrogen Bonding in a Collagen Model Peptide

Case

Baum

2015

Biochemistry

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“…3 NMA has thus been widely used to investigate the properties of the amide motif in various molecular environments both experimentally [4][5][6][7][8][9][10][11][12] and theoretically. [13][14][15][16][17][18][19] The vibrational relaxation dynamics of the amide modes of NMA have been studied before with infrared vibrational spectroscopy 8,10,[20][21][22] and with molecular dynamics simulations. 16,17,[23][24][25][26][27] All previous studies of the vibrational dynamics of NMA showed that the amide vibrations relax via intramolecular energy transfer, irrespective of the solvent used.…”

Section: Introductionmentioning

confidence: 99%

Vibrational relaxation pathways of amide I and amide II modes in N-methylacetamide

Piątkowski

Bakker

2012

The Journal of Chemical Physics

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We studied the vibrational energy relaxation mechanisms of the amide I and amide II modes of N-methylacetamide (NMA) monomers dissolved in bromoform using polarization-resolved femtosecond two-color vibrational spectroscopy. The results show that the excited amide I vibration transfers its excitation energy to the amide II vibration with a time constant of 8.3 ± 1 ps. In addition to this energy exchange process, we observe that the excited amide I and amide II vibrations both relax to a final thermal state. For the amide I mode this latter process dominates the vibrational relaxation of this mode. We find that the vibrational relaxation of the amide I mode depends on frequency which can be well explained from the presence of two subbands with different vibrational lifetimes (~1.1 ps on the low frequency side and ~2.7 ps on the high frequency side) in the amide I absorption spectrum.

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“…(1) has been established in our laboratory and has been successfully used to predict the intermolecular hydrogen bonding interactions in amide–amide, amide–thymine, and amide–uracil systems. [32–36] The first term of eq. (1) describes the dipole–dipole interaction.…”

Section: Theoretical Methodsmentioning

confidence: 99%

“…(1) to predict the intermolecular hydrogen‐bonding interactions in amide–amide, amide–thymine, and amide–uracil systems. [32–36] To further use eq. (1) to calculate the binding energies in amide–base systems in which NH···N and CH···N interactions exist, six hydrogen‐bonded amide–base dimers (Fig.…”

Section: Theoretical Methodsmentioning

confidence: 99%

“…An analytic potential energy function for hydrogen bonds has been established in our laboratory and has been successfully used to calculate the binding energies for a series of simple hydrogen‐bonded dimers,[32] β‐sheets,[33] the cooperativity in hydrogen bond chains,[34, 35] and the hydrogen‐bonded amide–thymine and amide–uracil dimers. [36] In this article, we further apply this analytic potential energy function to some hydrogen‐bonded peptide amide–DNA base systems.…”

Section: Introductionmentioning

confidence: 99%

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Rapid evaluation of the binding energies between peptide amide and DNA base

Liebeskind

Wang

2011

J Comput Chem

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The binding energies and the equilibrium hydrogen bond distances as well as the potential energy curves of 20 hydrogen-bonded amide-base dimers are evaluated from the analytic potential energy function established in our laboratory recently. The analytic potential energy function is used to calculate the N-H···N, N-H···O=C, C-H···N, and C-H···O=C dipole-dipole attractive interaction energies and C=O···O=C, N-H···H-N, and N-H···H-C dipole-dipole repulsive interaction energies in the 20 dimers composed of DNA bases adenine, guanine, cytosine, or thymine and peptide amide. The calculation results show that the potential energy curves obtained from the analytic potential energy function are in good agreement with those obtained from MP2/6-311+G** calculations by including the basis set superposition error (BSSE) correction. For all the 20 dimers, the analytic potential energy function yields the binding energies of the MP2/6-311+G** with BSSE correction within the error limits of 0.50 kcal/mol for 19 dimers, only one difference is larger than 0.50 kcal/mol and the difference is only 0.61 kcal/mol. The analytic potential energy function produces the equilibrium hydrogen bond distances of the MP2/6-311+G** with BSSE correction within the error limits of 0.030 Å for all the 20 dimers. The analytic potential energy function is further applied to four more complicated DNA base-peptide amide systems involving amino acid side chain and β-sheet. The values of the binding energies and equilibrium hydrogen bond distances obtained from the analytic potential energy function are also in good agreement with those obtained from MP2 calculations with the BSSE correction. These results demonstrate that the analytic potential energy function can be used to evaluate the binding energies in hydrogen-bonded peptide amide-DNA base dimers quickly and accurately.

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Rapid Prediction of the Hydrogen Bond Cooperativity inN‐methylacetamide Chains

Cited by 30 publications

References 73 publications

Dynamic Water-Mediated Hydrogen Bonding in a Collagen Model Peptide

Dynamic Water-Mediated Hydrogen Bonding in a Collagen Model Peptide

Vibrational relaxation pathways of amide I and amide II modes in N-methylacetamide

Rapid evaluation of the binding energies between peptide amide and DNA base

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