scholarly journals Toward quantification of protein backbone-backbone hydrogen bonding energies: An energetic analysis of an amide-to-ester mutation in an α-helix within a protein

2008 ◽  
Vol 17 (6) ◽  
pp. 1096-1101 ◽  
Author(s):  
Jianmin Gao ◽  
Jeffery W. Kelly
Keyword(s):  
Hydrogen Bonding ◽  
Protein Backbone ◽  
Energetic Analysis ◽  
Α Helix

Structure, stability and folding of the α-helix

2001 ◽  
Vol 68 ◽  
pp. 95-110 ◽  
Author(s):  
Andrew J. Doig ◽  
Charles D. Andrew ◽  
Duncan A. E. Cochran ◽  
Eleri Hughes ◽  
Simon Penel ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Hydrophobic Interactions ◽  
Data Bank ◽  
Site Directed Mutagenesis ◽  
Model Systems ◽  
Side Chain ◽  
Structure Stability ◽  
Helical Peptides ◽  
Vast Number ◽  
Α Helix

Pauling first described the α-helix nearly 50 years ago, yet new features of its structure continue to be discovered, using peptide model systems, site-directed mutagenesis, advances in theory, the expansion of the Protein Data Bank and new experimental techniques. Helical peptides in solution form a vast number of structures, including fully helical, fully coiled and partly helical. To interpret peptide results quantitatively it is essential to use a helix/coil model that includes the stabilities of all these conformations. Our models now include terms for helix interiors, capping, side-chain interactions, N-termini and 310-helices. The first three amino acids in a helix (N1, N2 and N3) and the preceding N-cap are unique, as their amide NH groups do not participate in backbone hydrogen bonding. We surveyed their structures in proteins and measured their amino acid preferences. The results are predominantly rationalized by hydrogen bonding to the free NH groups. Stabilizing side-chain-side-chain energies, including hydrophobic interactions, hydrogen bonding and polar/non-polar interactions, were measured accurately in helical peptides. Helices in proteins show a preference for having approximately an integral number of turns so that their N- and C-caps lie on the same side. There are also strong periodic trends in the likelihood of terminating a helix with a Schellman or αL C-cap motif. The kinetics of α-helix folding have been studied with stopped-flow deep ultraviolet circular dichroism using synchrotron radiation as the light source; this gives a far superior signal-to-noise ratio than a conventional instrument. We find that poly(Glu), poly(Lys) and alanine-based peptides fold in milliseconds, with longer peptides showing a transient overshoot in helix content.

scholarly journals Direct NMR Detection of Bifurcated Hydrogen Bonding in the α-Helix N-Caps of Ankyrin Repeat Proteins

2015 ◽  
Vol 137 (3) ◽  
pp. 1008-1011 ◽  
Author(s):  
Matthew R. Preimesberger ◽  
Ananya Majumdar ◽  
Tural Aksel ◽  
Kevin Sforza ◽  
Thomas Lectka ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Ankyrin Repeat ◽  
Repeat Proteins ◽  
Ankyrin Repeat Proteins ◽  
Α Helix

Calculation of the CONH dipole contribution to lattice energies of amides, polyamides, and polypeptides

1964 ◽  
Vol 278 (1372) ◽  
pp. 91-109 ◽  
Keyword(s):  
Hydrogen Bonding ◽  
Total Energy ◽  
Lattice Energy ◽  
Nylon 6 ◽  
Kcal Mole ◽  
Protein Molecules ◽  
Lattice Energies ◽  
The Stability ◽  
Α Helix ◽  
Dipole Energy

The dipole energy of a lattice of point dipoles in the configurations of the polyamides 6.6 and 6, of tetradecanamide, and of α and β forms of poly-L-alanine are calculated. The dipole forces contribute 4·8 kcal/mole to the lattice energy of nylon 6.6 of which 93 % arises from the collinear arrays of CONH dipoles along the ‘ a ’ axis. For nylon 6 the total energy is 4·6 kcal/ mole. In tetradecanamide the total energy is 3·9 kcal/mole of which only 0·7 kcal/mole arise from the dimer pairs of CONH 2 groups. The calculated energy for β poly-L-alanine is 5·7 kcal/ mole but only 1·8 kcal/mole for the α helix. The dipole forces only stablize the α helix for molecules containing more than 14 CONH groups. Below this length the dipole energy is repulsive. CO...HN hydrogen bonding contributes to the stability of the helix. Changes in configuration of protein molecules from α to β forms are probably facilitated by a balance between dipole forces and hydrogen bonding which vary reciprocally with changing configurations of the CONH group contacts.

scholarly journals Molecular mechanism of activation of human musk receptors OR5AN1 and OR1A1 by (R)-muscone and diverse other musk-smelling compounds

2018 ◽  
Vol 115 (17) ◽  
pp. E3950-E3958 ◽  
Author(s):  
Lucky Ahmed ◽  
Yuetian Zhang ◽  
Eric Block ◽  
Michael Buehl ◽  
Michael J. Corr ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Molecular Mechanism ◽  
Hybrid Methods ◽  
Hydrophobic Interactions ◽  
Structural Models ◽  
Quantitative Structure Activity Relationship ◽  
Binding Energies ◽  
Site Directed Mutagenesis ◽  
Aromatic Residues ◽  
Α Helix

Understanding olfaction at the molecular level is challenging due to the lack of crystallographic models of odorant receptors (ORs). To better understand the molecular mechanism of OR activation, we focused on chiral (R)-muscone and other musk-smelling odorants due to their great importance and widespread use in perfumery and traditional medicine, as well as environmental concerns associated with bioaccumulation of musks with estrogenic/antiestrogenic properties. We experimentally and computationally examined the activation of human receptors OR5AN1 and OR1A1, recently identified as specifically responding to musk compounds. OR5AN1 responds at nanomolar concentrations to musk ketone and robustly to macrocyclic sulfoxides and fluorine-substituted macrocyclic ketones; OR1A1 responds only to nitromusks. Structural models of OR5AN1 and OR1A1 based on quantum mechanics/molecular mechanics (QM/MM) hybrid methods were validated through direct comparisons with activation profiles from site-directed mutagenesis experiments and analysis of binding energies for 35 musk-related odorants. The experimentally found chiral selectivity of OR5AN1 to (R)- over (S)-muscone was also computationally confirmed for muscone and fluorinated (R)-muscone analogs. Structural models show that OR5AN1, highly responsive to nitromusks over macrocyclic musks, stabilizes odorants by hydrogen bonding to Tyr260 of transmembrane α-helix 6 and hydrophobic interactions with surrounding aromatic residues Phe105, Phe194, and Phe207. The binding of OR1A1 to nitromusks is stabilized by hydrogen bonding to Tyr258 along with hydrophobic interactions with surrounding aromatic residues Tyr251 and Phe206. Hydrophobic/nonpolar and hydrogen bonding interactions contribute, respectively, 77% and 13% to the odorant binding affinities, as shown by an atom-based quantitative structure–activity relationship model.

scholarly journals Control of conformation in α-helix mimicking aromatic oligoamide foldamers through interactions between adjacent side-chains

2019 ◽  
Vol 17 (15) ◽  
pp. 3861-3867 ◽  
Author(s):  
Irene Arrata ◽  
Claire M. Grison ◽  
Heather M. Coubrough ◽  
Panchami Prabhakaran ◽  
Marc A. Little ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Side Chains ◽  
Hydrogen Bonding Interactions ◽  
Α Helix

Hydrogen-bonding interactions are used to bias the conformation of an aromatic oligoamide foldamer in favour of an α-helix mimicking syn conformer.

Side-Chain Orientation and Hydrogen-Bonding Imprint Supra-τc Motion on the Protein Backbone of Ubiquitin

2005 ◽  
Vol 117 (47) ◽  
pp. 7954-7956 ◽  
Author(s):  
Nils A. Lakomek ◽  
Christophe Farès ◽  
Stefan Becker ◽  
Teresa Carlomagno ◽  
Jens Meiler ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Side Chain ◽  
Protein Backbone ◽  
Chain Orientation ◽  
Side Chain Orientation

scholarly journals A detailed picture of a protein–carbohydrate hydrogen-bonding network revealed by NMR and MD simulations

Glycobiology ◽  
2020 ◽  
Author(s):  
Gustav Nestor ◽  
Alessandro Ruda ◽  
Taigh Anderson ◽  
Stefan Oscarson ◽  
Göran Widmalm ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Antiviral Agents ◽  
Md Simulations ◽  
Protein Backbone ◽  
Carbohydrate Ligands ◽  
Hydrogen Bonding Network ◽  
Dynamics Simulations ◽  
Hydroxyl Protons

Abstract Cyanovirin-N (CV-N) is a cyanobacterial lectin with antiviral activity towards HIV and several other viruses. Here, we identify mannoside hydroxyl protons that are hydrogen bonded to the protein backbone of the CV-N domain B binding site, using NMR spectroscopy. For the two carbohydrate ligands Manα(1→2)ManαOMe and Manα(1→2) Manα(1→6)ManαOMe five hydroxyl protons are involved in hydrogen-bonding networks. Comparison with previous crystallographic results revealed that four of these hydroxyl protons donate hydrogen bonds to protein backbone carbonyl oxygens in solution and in the crystal. Hydrogen bonds were not detected between the side chains of Glu41 and Arg76 with sugar hydroxyls, as previously proposed for CV-N binding of mannosides. Molecular dynamics simulations of the CV-N/Manα(1→2)Manα(1→6)ManαOMe complex confirmed the NMR-determined hydrogen-bonding network. Detailed characterization of CV-N/mannoside complexes provides a better understanding of lectin-carbohydrate interactions and opens up to the use of CV-N and similar lectins as antiviral agents.

Side-Chain Orientation and Hydrogen-Bonding Imprint Supra-τc Motion on the Protein Backbone of Ubiquitin

2005 ◽  
Vol 44 (47) ◽  
pp. 7776-7778 ◽  
Author(s):  
Nils A. Lakomek ◽  
Christophe Farès ◽  
Stefan Becker ◽  
Teresa Carlomagno ◽  
Jens Meiler ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Side Chain ◽  
Protein Backbone ◽  
Chain Orientation ◽  
Side Chain Orientation
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