pH Dependence of hydrogen bonding in complexes between trimethyl-N-oxide and pentachlorophenol and trifluoroacetic acid in acetonitrile

1984 ◽  
Vol 80 (7) ◽  
pp. 1757 ◽  
Author(s):  
Zenon Pawlak ◽  
Maria Tusk ◽  
Stefan Kuna ◽  
Frank Strohbusch ◽  
Malcolm F. Fox
Keyword(s):  
Hydrogen Bonding ◽  
Trifluoroacetic Acid ◽  
Ph Dependence

scholarly journals pH-controlled hydrogen-bonding (Short Communication)

1974 ◽  
Vol 143 (3) ◽  
pp. 775-777 ◽  
Author(s):  
John L. Wood
Keyword(s):  
Hydrogen Bonding ◽  
Dissociation Constant ◽  
Small Proportion ◽  
Association Constant ◽  
Short Communication ◽  
Dibasic Acid ◽  
Ph Dependence ◽  
Ph Values ◽  
Conjugate Acid ◽  
Total Base

The pH-dependence of the degree of hydrogen-bonding between a base and its conjugate acid is considered. When only a small proportion of the total base is complexed, the amount complexed is proportional to (1+coshp)−1 where p=2.303 (pKa–pH), pKa being the dissociation constant of the conjugate acid. This represents sharp pH-dependence. As the proportion complexed increases, the curve broadens, eventually becoming flat-topped, with more than half the base complexed over the range of pH values pKa±logKC, approximately. (K is the complex association constant and C is the formal base concentration, including all forms.) There are similarities to the extent of mono-protonation of a dibasic acid.

scholarly journals The interplay of electrostatic fields and binding interactions determining catalytic-site reactivity in actinidin. A possible origin of differences in the behaviour of actinidin and papain

1989 ◽  
Vol 259 (2) ◽  
pp. 443-452 ◽  
Author(s):  
D Kowlessur ◽  
M O'Driscoll ◽  
C M Topham ◽  
W Templeton ◽  
E W Thomas ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Ligand Binding ◽  
Transition State ◽  
Rate Constant ◽  
Ph Dependence ◽  
Order Rate Constant ◽  
Catalytic Site ◽  
Binding Interactions ◽  
Electrostatic Fields ◽  
Transition State Geometry

1. The pH-dependence of the second-order rate constant (k) for the reaction of actinidin (EC 3.4.22.14) with 2-(N'-acetyl-L-phenylalanylamino)ethyl 2'-pyridyl disulphide was determined and the contributions to k of various hydronic states were evaluated. 2. The data were used to assess the consequences for transition-state geometry of providing P2/S2 hydrophobic contacts in addition to hydrogen-bonding opportunities in the S1-S2 intersubsite region. 3. The P2/S2 contacts (a) substantially improve enzyme-ligand binding, (b) greatly enhance the contribution to reactivity of the hydronic state bounded by pKa 3 (the pKa characteristic of the formation of catalytic-site-S-/-ImH+ state) and pKa 5 (a relatively minor contributor in reactions that lack the P2/S2 contacts), such that the major rate optimum occurs at pH 4 instead of at pH 2.8-2.9, and (c) reveal the kinetic influence of a pKa approx. 6.3 not hitherto observed in reactions of actinidin. 4. Possibilities for the interplay of electrostatic effects and binding interactions in both actinidin and papain (EC 3.4.22.2) are discussed.

scholarly journals Changes in active site histidine hydrogen bonding trigger cryptochrome activation

2016 ◽  
Vol 113 (36) ◽  
pp. 10073-10078 ◽  
Author(s):  
Abir Ganguly ◽  
Craig C. Manahan ◽  
Deniz Top ◽  
Estella F. Yee ◽  
Changfan Lin ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Conformational Changes ◽  
Large Scale ◽  
Ph Dependence ◽  
Md Simulations ◽  
Cellular Assays ◽  
Hydrogen Bonding Pattern ◽  
Poisson Boltzmann ◽  
Active Site Histidine ◽  
Clock Protein

Cryptochrome (CRY) is the principal light sensor of the insect circadian clock. Photoreduction of the Drosophila CRY (dCRY) flavin cofactor to the anionic semiquinone (ASQ) restructures a C-terminal tail helix (CTT) that otherwise inhibits interactions with targets that include the clock protein Timeless (TIM). All-atom molecular dynamics (MD) simulations indicate that flavin reduction destabilizes the CTT, which undergoes large-scale conformational changes (the CTT release) on short (25 ns) timescales. The CTT release correlates with the conformation and protonation state of conserved His378, which resides between the CTT and the flavin cofactor. Poisson-Boltzmann calculations indicate that flavin reduction substantially increases the His378 pKa. Consistent with coupling between ASQ formation and His378 protonation, dCRY displays reduced photoreduction rates with increasing pH; however, His378Asn/Arg variants show no such pH dependence. Replica-exchange MD simulations also support CTT release mediated by changes in His378 hydrogen bonding and verify other responsive regions of the protein previously identified by proteolytic sensitivity assays. His378 dCRY variants show varying abilities to light-activate TIM and undergo self-degradation in cellular assays. Surprisingly, His378Arg/Lys variants do not degrade in light despite maintaining reactivity toward TIM, thereby implicating different conformational responses in these two functions. Thus, the dCRY photosensory mechanism involves flavin photoreduction coupled to protonation of His378, whose perturbed hydrogen-bonding pattern alters the CTT and surrounding regions.

HYDROGEN BONDING IN SOLUTIONS OF SUBSTITUTED ACETIC ACIDS

1961 ◽  
Vol 39 (8) ◽  
pp. 1711-1720 ◽  
Author(s):  
Leonard W. Reeves
Keyword(s):  
Hydrogen Bonding ◽  
Chemical Shift ◽  
Carboxylic Acids ◽  
Trifluoroacetic Acid ◽  
Dimethyl Formamide ◽  
Acid Solutions ◽  
Dilute Solution ◽  
Acid Proton ◽  
Solvent Molecules ◽  
Acetic Acids

The changes in chemical shift of the acid proton in some simple carboxylic acids on dilution in four solvents has been studied. The existence of chainlike hydrogen-bonded polymers in solution is suggested by the results. The association of the monomer molecules in dilute solution with donor centers in the solvent molecules is suggested from a study of the —O—H monomer stretching bond in the vapor and in two solvents. There is a difference in the behavior of acetic and trifluoroacetic acid in N-methyl and N,N-dimethyl formamide, which has been explained in terms of protonation of the amides in trifluoroacetic acid solutions.

scholarly journals Expression and characterization of Pseudomonas aeruginosa cytochrome c-551 and two site-directed mutants: role of tryptophan 56 in the modulation of redox properties

1997 ◽  
Vol 322 (1) ◽  
pp. 35-42 ◽  
Author(s):  
Francesca CUTRUZZOLÀ ◽  
Ilaria CIABATTI ◽  
Gabriella ROLLI ◽  
Sabrina FALCINELLI ◽  
Marzia ARESE ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Cytochrome C ◽  
Ph Dependence ◽  
Redox Properties ◽  
Expression Vectors ◽  
Wild Type ◽  
Type Protein ◽  
Wild Type Protein ◽  
Structural And Functional Properties

The gene coding for Pseudomonas aeruginosacytochrome c-551 was expressed in Pseudomonas putidaunder aerobic conditions, using two different expression vectors; the more efficient proved to be pNM185, induced by m-toluate. Mature holo-(cytochrome c-551) was produced in high yield by this expression system, and was purified to homogeneity. Comparison of the recombinant wild-type protein with that purified from Ps. aeruginosashowed no differences in structural and functional properties. Trp56, an internal residue in cytochrome c-551, is located at hydrogen-bonding distance from haem propionate-17, together with Arg47. Ionization of propionate-17 was related to the observed pH-dependence of redox potential. The role of Trp56 in determining the redox properties of Ps. aeruginosacytochrome c-551 was assessed by site-directed mutagenesis, by substitution with Tyr (W56Y) and Phe (W56F). The W56Y mutant is similar to the wild-type cytochrome. On the other hand, the W56F mutant, although similar to the wild-type protein in spectral properties and electron donation to azurin, is characterized by a weakening of the FeŐMet61 bond, as shown in the oxidized protein by the loss of the 695 nm band approx. 2 pH units below the wild-type. Moreover, in W56F, the midpoint potential and its pH-dependence are both different from the wild-type. These results are consistent with the hypothesis that hydrogen-bonding to haem propionate-17 is important in modulation of the redox properties of Ps. aeruginosacytochrome c-551.

scholarly journals Carboxyl pKa Values, Ion Pairs, Hydrogen Bonding, and the pH-dependence of Folding the Hyperthermophile Proteins Sac7d and Sso7d

2007 ◽  
Vol 372 (4) ◽  
pp. 992-1008 ◽  
Author(s):  
Andrew T. Clark ◽  
Kelley Smith ◽  
Ranjith Muhandiram ◽  
Stephen P. Edmondson ◽  
John W. Shriver
Keyword(s):  
Hydrogen Bonding ◽  
Ph Dependence ◽  
Ion Pairs ◽  
Pka Values
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