scholarly journals Combined Covalent-Electrostatic Model of Hydrogen Bonding Improves Structure Prediction with Rosetta

2015 ◽  
Vol 11 (2) ◽  
pp. 609-622 ◽  
Author(s):  
Matthew J. O’Meara ◽  
Andrew Leaver-Fay ◽  
Michael D. Tyka ◽  
Amelie Stein ◽  
Kevin Houlihan ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Structure Prediction ◽  
Electrostatic Model

scholarly journals Tight Turns of Outer Membrane Proteins: An Analysis of Sequence, Structure, and Hydrogen Bonding

2018 ◽  
Author(s):  
Meghan Whitney Franklin ◽  
Joanna S.G. Slusky
Keyword(s):  
Hydrogen Bonding ◽  
Membrane Proteins ◽  
Outer Membrane ◽  
Soluble Protein ◽  
Structure Prediction ◽  
Outer Membrane Proteins ◽  
Sequence Structure ◽  
Structural Class ◽  
Future Design ◽  
Extracellular Loops

I.AbstractAs a structural class, tight turns can control molecular recognition, enzymatic activity, and nucleation of folding. They have been extensively characterized in soluble proteins but have not been characterized in outer membrane proteins (OMPs), where they also support critical functions. We clustered the 4-6 residue tight turns of 110 OMPs to characterize the phi/psi angles, sequence, and hydrogen bonding of these structures. We find significant differences between reports of soluble protein tight turns and OMP tight turns. Since OMP strands are less twisted than soluble strands they favor different turn structures types. Moreover, the membrane localization of OMPs yields different sequence hallmarks for their tight turns relative to soluble protein turns. We also characterize the differences in phi/psi angles, sequence, and hydrogen bonding between OMP extracellular loops and OMP periplasmic turns. As previously noted, the extracellular loops tend to be much longer than the periplasmic turns. We find that this difference in length is due to the broader distribution of lengths of the extracellular loops not a large difference in the median length. Extracellular loops also tend to have more charged residues as predicted by the charge-out rule. Finally, in all OMP tight turns, hydrogen bonding between the sidechain and backbone two to four residues away plays an important role. These bonds preferentially use an Asp, Asn, Ser or Thr residue in a beta or pro phi/psi conformation. We anticipate that this study will be applicable to future design and structure prediction of OMPs.

Anion-molecule complexes in solution. II. The complexing of halide ions with acetylated β-D-glucopyranosyl derivatives

1968 ◽  
Vol 46 (20) ◽  
pp. 3263-3274 ◽  
Author(s):  
J. S. Martin ◽  
Jun-Ichi Hayami ◽  
R. U. Lemieux
Keyword(s):  
Hydrogen Bonding ◽  
Equilibrium Constants ◽  
Strong Dependence ◽  
Electrostatic Model ◽  
Halide Ions ◽  
Pyranose Ring

Tetra-O-acetyl-β-D-glucopyranosyl halides and phenoxides in solution in acetonitrile showed a specific deshielding of H-1, H-3, and H-5 on addition of tetraethylammonium halides. The shifts and equilibrium constants increased as the anion radius decreased. The ortho hydrogens of the phenoxide aglucons were also significantly deshielded. The strong dependence of the equilibrium constants of the phenoxide compounds on p-substituents indicated considerable involvement of the phenyl groups in a specific conformation. A simple electrostatic model was successful in correlating the energies and predicting the structures of the complexes. It was not necessary to postulate specific hydrogen bonding to account for association of the anion with an electrophilic region of the molecule. The calculations required specific orientations of acetoxy groups with respect to the pyranose ring which are consistent with those of related studies. In favorable circumstances, the method may be used as a probe for electrophilic regions in molecules.

X-Ray Photoelectron Spectra of Aluminum Oxides: Structural Effects on the “Chemical Shift”

1973 ◽  
Vol 27 (1) ◽  
pp. 1-5 ◽  
Author(s):  
James R. Lindsay ◽  
Harry J. Rose ◽  
William E. Swartz ◽  
Plato H. Watts ◽  
Kenneth A. Rayburn
Keyword(s):  
Hydrogen Bonding ◽  
Binding Energy ◽  
Binding Energies ◽  
Photoelectron Spectra ◽  
Electrostatic Model ◽  
Structural Effects ◽  
Aluminum Oxides ◽  
X Ray ◽  
Structural Differences ◽  
Core Electrons

The aluminum (2p) electron spectra of several anhydrous and “hydrous” aluminum oxides have been recorded, and the binding energies have been measured. A simple electrostatic model is employed to explain the observed shift in binding energy and relate it to differences in structure and hydrogen bonding. Two conclusions can be drawn: structural differences must be considered when interpreting photoelectron spectra for inorganic crystalline substances; and hydrogen bonding with anions may have a measurable effect on the binding energy of core electrons of the cations.

scholarly journals Solvent inclusion in the crystal structure of bis[(adamantan-1-yl)methanaminium chloride] 1,4-dioxane hemisolvate monohydrate explained using the computed crystal energy landscape

2016 ◽  
Vol 72 (9) ◽  
pp. 1348-1352 ◽  
Author(s):  
Sharmarke Mohamed
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Structure Prediction ◽  
Unit Cell Volume ◽  
Energy Landscape ◽  
Lattice Energy ◽  
Low Energy ◽  
Energy Minimum ◽  
Crystal Structure Prediction ◽  
Hydrogen Bonding Interactions

Repeated attempts to crystallize 1-adamantanemethylamine hydrochloride as an anhydrate failed but the salt was successfully crystallized as a solvate (2C11H20N+·2Cl−·0.5C4H8O2·H2O), with water and 1,4-dioxane playing a structural role in the crystal and engaging in hydrogen-bonding interactions with the cation and anion. Computational crystal-structure prediction was used to rationalize the solvent-inclusion behaviour of this salt by computing the solvent-accessible voids in the predicted low-energy structures for the anhydrate: the global lattice-energy minimum structure, which has the same packing of the ions as the solvate, has solvent-accessible voids that account for 3.71% of the total unit-cell volume and is 6 kJ mol−1more stable than the next most stable predicted structure.

scholarly journals Protein structure prediction: Do hydrogen bonding and water-mediated interactions suffice?

Methods ◽  
2010 ◽  
Vol 52 (1) ◽  
pp. 84-90 ◽  
Author(s):  
Vanessa Oklejas ◽  
Chenghang Zong ◽  
Garegin A. Papoian ◽  
Peter G. Wolynes
Keyword(s):  
Hydrogen Bonding ◽  
Protein Structure ◽  
Protein Structure Prediction ◽  
Structure Prediction

scholarly journals Understanding the formation of apremilast cocrystals

2019 ◽  
Vol 75 (5) ◽  
pp. 803-814 ◽  
Author(s):  
Marta K. Dudek ◽  
Ewelina Wielgus ◽  
Piotr Paluch ◽  
Justyna Śniechowska ◽  
Maciej Kostrzewa ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Structure Prediction ◽  
Crystal Forms ◽  
X Ray Crystallography ◽  
High Propensity ◽  
Free Energy Of Formation ◽  
Stabilization Energies ◽  
Almost All ◽  
Entropic Stabilization

Apremilast (APR), an anti-psoriatic agent, easily forms isostructural cocrystals and solvates with aromatic entities, often disobeying at the same time Kitaigorodsky's rule as to the saturation of possible hydrogen-bonding sites. In this paper the reasons for this peculiar behavior are investigated, employing a joint experimental and theoretical approach. This includes the design of cocrystals with coformers having a high propensity towards the formation of both aromatic–aromatic and hydrogen-bonding interactions, determination of their structure, using solid-state NMR spectroscopy and X-ray crystallography, as well as calculations of stabilization energies of formation of the obtained cocrystals, followed by crystal structure prediction calculations and solubility measurements. The findings indicate that the stabilization energies of cocrystal formation are positive in all cases, which results from strain in the APR conformation in these crystal forms. On the other hand, solubility measurements show that the Gibbs free energy of formation of the apremilast:picolinamide cocrystal is negative, suggesting that the formation of the studied cocrystals is entropy driven. This entropic stabilization is associated with the disorder observed in almost all known cocrystals and solvates of APR.

THE STUDY OF HYDROGEN BONDING AND RELATED PHENOMENA BY ULTRAVIOLET LIGHT ABSORPTION: PART V. INTRAMOLECULAR HYDROGEN BONDING IN ANILINES AND PHENOLS

1960 ◽  
Vol 38 (10) ◽  
pp. 1837-1851 ◽  
Author(s):  
J. C. Dearden ◽  
W. F. Forbes
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Intramolecular Hydrogen Bond ◽  
Light Absorption ◽  
Intramolecular Hydrogen Bonding ◽  
Electrostatic Model ◽  
Spectral Change ◽  
Substituted Phenols ◽  
Spectral Changes ◽  
Intramolecular Hydrogen

Information concerning intramolecular hydrogen bonding in phenols and anilines can be obtained from ultraviolet spectra by a variety of methods. One method is to note the spectral changes observed between the corresponding o-substituted phenols and anisoles. A second method is to compare the spectral changes between o-substituted phenols or anilines and the corresponding meta isomers. A third method is to note the absence of an appreciable spectral change, on altering the solvent conditions, which may also indicate the formation of an intramolecular hydrogen bond. The conclusions deduced from the three methods confirm previously stated generalizations concerning the nature of the hydrogen bond. One notable exception is that the spectral changes ascribed to the intramolecular hydrogen bond in o-nitrophenol can be explained in terms of an electrostatic model of the hydrogen bond.

Electrostatic lock-and-key model for the analysis of inhibitor recognition by dihydrofolate reductase

1985 ◽  
Vol 63 (7) ◽  
pp. 1694-1698 ◽  
Author(s):  
Péter Nagy ◽  
Gábor Náray-Szabó
Keyword(s):  
Hydrogen Bonding ◽  
Dihydrofolate Reductase ◽  
Active Site ◽  
Ion Pair ◽  
Reference Points ◽  
Electrostatic Model ◽  
Enzyme Active Site ◽  
Key Accounts ◽  
Inhibitor Recognition ◽  
Pair Interactions

We propose a simple electrostatic model for the analysis of ligand binding to proteins. Besides a geometric fit electrostatic complementarity is also needed to allow favourable hydrogen bonding and ion-pair interactions. Nonpolar regions of the ligand and the biomacromolecule active site should match to reduce unfavourable hydrophobic effects, i.e., to lower the Gibbs free energy of the complex in aqueous solution. These principles are applied to the inhibition of dihydrofolate reductase by methotrexate. The enzyme active site is represented by an electrostatic lock which is derived from the macromolecular electrostatic potential and field at certain reference points. The key, defined similarly for the ligand, should fit into the lock to ensure complementarity, i.e., recognition. Hydrogen bonding and ion-pair interactions can be studied by the "potential key" while the "field key" accounts for hydrophobic complementarity. Analyzing the dihydrofolate reductase–methotrexate interaction in the light of the above principles the relative importance of various molecular fragments in binding can be determined.

Sign in / Sign up

Export Citation Format

Share Document