A MOLECULAR RECOGNITION MODEL FOR ENANTIOSELECTIVITY AND AUTOINDUCTION IN CYANOHYDRIN FORMATION CATALYZED BY CYCLO[(S)-HIS-(S)-PHE]

2010 ◽  
Vol 09 (02) ◽  
pp. 495-510
Author(s):  
JIAHAI WANG
Keyword(s):  
Molecular Recognition ◽  
Hydrogen Bonds ◽  
Theoretical Calculation ◽  
Am1 Method ◽  
Cyanide Ion ◽  
Recognition Mechanism ◽  
Ring Complex ◽  
Ring Complexes ◽  
Experimental Findings ◽  
Intramolecular Hydrogen

A molecular recognition mechanism based on dimeric model for cyclic dipeptide Cyclo[(S)-His-(S)-Phe] (abridged CHP) catalyzed autoinduction is proposed according to the inference of previous experimental findings, which is supported by theoretical calculation with Oniom(B3LYP/3-21G*:AM1) method. The most unstable CHP dimer whose intermolecular hydrogen bonds are immensely lessened by two intramolecular hydrogen bonds is defined as the highest active component (IIa) existing in solid among the three possible dimers (Ia, IIa, and IIb). The carbonyl group of benzaldehyde coordinates to CHP dimer (IIa) by a hydrogen bond with Phe–NαH rather than His–NαH and HCN interacted with the imidazole moiety of His residue to form cyanide ion. In view of the theoretical calculation and experimental results, the structures of the nine-ring complexes derived from interaction between catalytic active dimer CHP(IIa) and cyanohydrins were postulated to explain the enantioselective autoinduction: The structure of no nitrile involved six-ring complex derived from interaction between catalytic active dimer CHP(IIa) and cyanohydrins were postulated to explain the elimination of enantioselective autoinduction.

scholarly journals Molecular basis of flexible peptide recognition by an antibody

2020 ◽  
Vol 167 (4) ◽  
pp. 343-345
Author(s):  
Koki Makabe
Keyword(s):  
Hydrogen Bonds ◽  
High Specificity ◽  
Recognition Mechanism ◽  
Intramolecular Hydrogen Bonds ◽  
Peptide Recognition ◽  
X Ray Crystallography ◽  
Biophysical Techniques ◽  
Antibody Design ◽  
Dynamics Simulations ◽  
Intramolecular Hydrogen

Abstract Antibodies can recognize various types of antigens with high specificity and affinity and peptide is one of their major targets. Understanding an antibody’s molecular recognition mechanism for peptide is important for developing clones with a higher specificity and affinity. Here, the author reviews recent progresses in flexible peptide recognition by an antibody using several biophysical techniques, including X-ray crystallography, molecular dynamics simulations and calorimetric measurements. A set of two reports highlight the importance of intramolecular hydrogen bonds that form in an unbound flexible state. Such intramolecular hydrogen bonds restrict the fluctuation of the peptide and reduce the conformational entropy, resulting in the destabilization of the unbound state and increasing the binding affinity by increasing the free energy change. These detailed analyses will aid in the antibody design in the future.

Influence of remote intramolecular hydrogen bonds on the thermodynamics of molecular recognition of cis-1,3,5-cyclohexanetricar☐ylic acid

1999 ◽  
Vol 40 (1) ◽  
pp. 171-174 ◽  
Author(s):  
Pablo Ballester ◽  
Antoni Costa ◽  
Pere M. Deyà ◽  
Manuel Vega ◽  
Jeroni Morey ◽  
...  
Keyword(s):  
Molecular Recognition ◽  
Hydrogen Bonds ◽  
Ylic Acid ◽  
Intramolecular Hydrogen Bonds ◽  
Intramolecular Hydrogen

Controlling emissive properties by intramolecular hydrogen bonds: alkyl and aryl meso‐substituted porphycenes

2021 ◽  
Author(s):  
Jacek Waluk ◽  
Arkadiusz Listkowski ◽  
Natalia Masiera ◽  
Michał Kijak ◽  
Roman Luboradzki ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Intramolecular Hydrogen Bonds ◽  
Intramolecular Hydrogen

Energies of intramolecular hydrogen bonds in some alcohols

1974 ◽  
Vol 20 (3) ◽  
pp. 414-415
Author(s):  
Ya. A. Shuster ◽  
V. A. Granzhan ◽  
P. M. Zaitsev
Keyword(s):  
Hydrogen Bonds ◽  
Intramolecular Hydrogen Bonds ◽  
Intramolecular Hydrogen

scholarly journals X-ray crystallography reveals molecular recognition mechanism for sugar binding in a melibiose transporter MelB

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Lan Guan ◽  
Parameswaran Hariharan
Keyword(s):  
Molecular Recognition ◽  
Binding Pocket ◽  
Cation Binding ◽  
Recognition Mechanism ◽  
X Ray ◽  
X Ray Crystallography ◽  
Sugar Binding ◽  
Sugar Specificity ◽  
Major Facilitator ◽  
Mfs Transporters

AbstractMajor facilitator superfamily_2 transporters are widely found from bacteria to mammals. The melibiose transporter MelB, which catalyzes melibiose symport with either Na+, Li+, or H+, is a prototype of the Na+-coupled MFS transporters, but its sugar recognition mechanism has been a long-unsolved puzzle. Two high-resolution X-ray crystal structures of a Salmonella typhimurium MelB mutant with a bound ligand, either nitrophenyl-α-d-galactoside or dodecyl-β-d-melibioside, were refined to a resolution of 3.05 or 3.15 Å, respectively. In the substrate-binding site, the interaction of both galactosyl moieties on the two ligands with MelBSt are virturally same, so the sugar specificity determinant pocket can be recognized, and hence the molecular recognition mechanism for sugar binding in MelB has been deciphered. The conserved cation-binding pocket is also proposed, which directly connects to the sugar specificity pocket. These key structural findings have laid a solid foundation for our understanding of the cooperative binding and symport mechanisms in Na+-coupled MFS transporters, including eukaryotic transporters such as MFSD2A.

scholarly journals Crystal structure of atazanavir, C38H52N6O7

2020 ◽  
Vol 35 (2) ◽  
pp. 129-135
Author(s):  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Powder Diffraction ◽  
Density Functional ◽  
Carbonyl Oxygen ◽  
Hydroxyl Group ◽  
Amide Nitrogen ◽  
Classical Hydrogen Bond ◽  
Intramolecular Hydrogen ◽  
Atazanavir Sulfate

The crystal structure of atazanavir has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional techniques. Atazanavir crystallizes in space group P21 (#4) with a = 15.33545(7), b = 5.90396(3), c = 21.56949(13) Å, β = 96.2923(4)°, V = 1941.134(11) Å3, and Z = 2. Despite being labeled as “atazanavir sulfate”, the commercial reagent sample consisted of atazanavir free base. The structure consists of an array of extended-conformation molecules parallel to the ac-plane. Although the atazanavir molecule contains only four classical hydrogen bond donors, hydrogen bonding is, surprisingly, important to the crystal energy. Both intra- and intermolecular hydrogen bonds are significant. The hydroxyl group forms bifurcated intramolecular hydrogen bonds to a carbonyl oxygen atom and an amide nitrogen. Several amide nitrogens act as donors to the hydroxyl group and carbonyl oxygen atoms. An amide nitrogen acts as a donor to another amide nitrogen. Several methyl, methylene, methyne, and phenyl hydrogens participate in hydrogen bonds to carbonyl oxygens, an amide nitrogen, and the pyridine nitrogen. The powder pattern is included in the Powder Diffraction File™ as entry 00-065-1426.

Hydrogen bonds in derivatives of N-substituted N’-benzoyl- and N’-(2-chlorobenzoyl)thiourea

1991 ◽  
Vol 56 (4) ◽  
pp. 880-885 ◽  
Author(s):  
Oľga Hritzová ◽  
Dušan Koščík
Keyword(s):  
Hydrogen Bonds ◽  
Spectral Studies ◽  
Intramolecular Hydrogen Bonds ◽  
Tautomeric Forms ◽  
Intramolecular Hydrogen ◽  
Derivatives Of

Intramolecular hydrogen bonds of the N-H···O=C type have been detected in the derivatives of N-substituted N’-benzoyl- and N’-(2-chlorobenzoyl)thiourea on the basis of IR spectral studies. The title compounds can exist in two tautomeric forms.

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