Formation Of Internal Hydrogen Bonds Research Articles

AMBER and CHARMM Force Fields Inconsistently Portray the Microscopic Details of Phosphorylation.

Phosphorylation of serine, threonine, and tyrosine is one of the most frequently occurring and crucial post-translational modifications of proteins often associated with important structural and functional changes. We investigated the direct effect of phosphorylation on the intrinsic conformational preferences of amino acids as a potential trigger of larger structural events. We conducted a comparative study of force fields on terminally capped amino acids (dipeptides) as the simplest model for phosphorylation. Our bias-exchange metadynamics simulations revealed that all model dipeptides sampled a great heterogeneity of ensembles affected by introduction of mono- and dianionic phosphate groups. However, the detected changes in populations of backbone conformers and side-chain rotamers did not reveal a strong discriminatory shift in preferences, as could be anticipated for the bulky, charged phosphate group. Furthermore, the AMBER and CHARMM force fields provided inconsistent populations of individual conformers as well as net structural trends upon phosphorylation. Detailed analysis of ensembles revealed competition between hydration and formation of internal hydrogen bonds involving amide hydrogens and the phosphate group. The observed difference in hydration free energy and potential for hydrogen bonding in individual force fields could be attributed to the different partial atomic charges used in each force field and, hence, the different parametrization strategies. Nevertheless, conformational propensities and net structural changes upon phosphorylation are difficult to extract from experimental measurements, and existing experimental data provide limited guidance for force field assessment and further development.

Backbone hydration determines the folding signature of amino acid residues.

The relation between the sequence of a protein and its three-dimensional structure remains largely unknown. A lasting dream is to elucidate the side-chain-dependent driving forces that govern the folding process. Different structural data suggest that aromatic amino acids play a particular role in the stabilization of protein structures. To better understand the underlying mechanism, we studied peptides of the sequence EGAAXAASS (X = Gly, Ile, Tyr, Trp) through comparison of molecular dynamics (MD) trajectories and NMR residual dipolar coupling (RDC) measurements. The RDC data for aromatic substitutions provide evidence for a kink in the peptide backbone. Analysis of the MD simulations shows that the formation of internal hydrogen bonds underlying a helical turn is key to reproduce the experimental RDC values. The simulations further reveal that the driving force leading to such helical-turn conformations arises from the lack of hydration of the peptide chain on either side of the bulky aromatic side chain, which can potentially act as a nucleation point initiating the folding process.

Aromatic Amino Acids Promote Peptide Folding by Reducing Backbone Hydration

The relation between the sequence of a protein and its tridimensional structure remains largely unknown. To better understand how single residues impact on the local protein structure, we studied peptides of sequence EGAAXAASS (X = Gly, Ile, Tyr, Trp) through comparison of molecular dynamics (MD) trajectories and NMR residual dipolar coupling (RDC) measurements. The RDC patterns of the peptide with X = Gly or Ile are rather flat, suggesting extended, unfolded peptides, while the contrasted patterns for peptides with X = Tyr or Trp suggest compact folded structures. The comparison shows that the formation of internal hydrogen bonds underlying helical-turns is key to reproduce experimental RDC values for the peptides containing aromatic residues. The simulations further reveal that the driving force leading to such helical-turn conformation arises from the lack of hydration of the peptide chain on either side of the bulky aromatic side chain, which can potentially act as a nucleation point initiating the folding process. These results provide a starting point to understand the amino acid code underlying the mechanism of protein folding.

Mastering the Canonical Loop of Serine Protease Inhibitors: Enhancing Potency by Optimising the Internal Hydrogen Bond Network

BackgroundCanonical serine protease inhibitors commonly bind to their targets through a rigid loop stabilised by an internal hydrogen bond network and disulfide bond(s). The smallest of these is sunflower trypsin inhibitor (SFTI-1), a potent and broad-range protease inhibitor. Recently, we re-engineered the contact β-sheet of SFTI-1 to produce a selective inhibitor of kallikrein-related peptidase 4 (KLK4), a protease associated with prostate cancer progression. However, modifications in the binding loop to achieve specificity may compromise structural rigidity and prevent re-engineered inhibitors from reaching optimal binding affinity.Methodology/Principal FindingsIn this study, the effect of amino acid substitutions on the internal hydrogen bonding network of SFTI were investigated using an in silico screen of inhibitor variants in complex with KLK4 or trypsin. Substitutions favouring internal hydrogen bond formation directly correlated with increased potency of inhibition in vitro. This produced a second generation inhibitor (SFTI-FCQR Asn14) which displayed both a 125-fold increased capacity to inhibit KLK4 (K i = 0.0386±0.0060 nM) and enhanced selectivity over off-target serine proteases. Further, SFTI-FCQR Asn14 was stable in cell culture and bioavailable in mice when administered by intraperitoneal perfusion.Conclusion/SignificanceThese findings highlight the importance of conserving structural rigidity of the binding loop in addition to optimising protease/inhibitor contacts when re-engineering canonical serine protease inhibitors.

Intramolecular Hydrogen Bonding in Disubstituted Ethanes. A Comparison of NH···O- and OH···O- Hydrogen Bonding through Conformational Analysis of 4-Amino-4-oxobutanoate (succinamate) and Monohydrogen 1,4-Butanoate (monohydrogen succinate) Anions

Relative strengths of amide NH...O- and carboxyl OH...O- hydrogen bonds were investigated via conformational analysis of succinamate and monohydrogen succinate anions with the aid of vicinal proton-proton NMR couplings and B3LYP DFT quantum mechanical calculations for a variety of solvents. New experimental results for succinamate are compared with those obtained from previous studies of monohydrogen succinate. While some computational results for monohydrogen succinate were published previously, the results contained herein are the product of a more powerful methodology than that used earlier. The experimental results clearly show that intramolecular hydrogen-bond formation is more favored in aprotic solvents than in protic solvents for both molecules. Furthermore, the preference of the succinate monoanion for the gauche conformation is much stronger in aprotic solvents than that of succinamate, indicating that the OH...O- hydrogen bond is substantially stronger than its NH...O- counterpart, despite the approximately 5 kcal cost for formation of the E configuration of the carboxyl group needed to make an intramolecular hydrogen bond. The actual energy differences between formation of internal hydrogen bonds for monohydrogen succinate and succinamate anion were estimated by comparison of the relative values of K1 of the respective acids in water and DMSO by a procedure first developed by Westheimer. Recent theoretical work with succinamate highlights the necessity of considering substituent orientational degrees of freedom to understand the conformational equilibria of the central CH2-CH2 torsions in disubstituted ethanes. Similar methodology is applied here to succinic acid monoanion, by mapping potential-energy surfaces with respect to the CH2-CH2 torsional, carboxyl-substituent rotational, and carboxyl-proton E/Z isomeric degrees of freedom. Boltzmann populations were compared with gauche populations estimated from the experimentally determined coupling constants. The quantum mechanical results for succinamate show a much weaker tendency toward hydrogen bonding than for the succinic acid monoanion. However, the theoretical methods employed appear to substantially overestimate contributions from intramolecularly hydrogen-bonded structures for the succinic acid monoanion when compared with experimental results. Natural bond orbital analysis, applied to the quantum mechanical wave functions of fully optimized gauche and trans structures, showed a strong correlation between the population of amide sigma*(N-H) and carboxyl sigma*(O-H) antibonding orbitals and apparent hydrogen-bonding behavior.

Structural requirements for rapid metal ion ingress into hydroxyethylated tetraaza macrocycles

Synthesis of two new bis(2-hydroxyethyl)_substituted cyclam (1,4,8,11-tetraazacyclotetradecane) 1,4-bis(2-hydroxyethyl)-8,11-dimethylcyclam (1,4-DMHEC-14) and 1,11-bis(2-hydroxyethyl)-4,8-dimethylcyclam (1,11-DMHEC-14), has enabled a study of the effects of partial hydroxyethylation of the nitrogen atoms in a macrocyclic ligand framework to be made. The ligands were synthesised through the reaction of ethylene oxide with the appropriately methylated cyclam precursor. Stability constants for complexes of these ligands with Co 2+, Ni 2+, Cu 2+, Zn 2+ Cd 2+ Hg 2+ and Pb 2+ have been measured by potentiometric titration and are generally intermediate between those shown by tetramethylcyclam (TMC-14) and tetrakis(2-hydroxyethyl)cyclam (THEC-14), consistent with a lower level of ligand stabilisation through internal hydrogen bond formation than in THEC-14. Equilibration times noted during the potentiometric titrations indicate that these bis(2-hydroxyethyl) ligands, like THEC-14 and unlike TMC-14, facilitate rapid entry of the metal ion into the macrocyclic annulus demonstrating that two pendant 2-hydroxyethyl arms, when located on adjacent nitrogen atoms, are sufficient to generate facilitated entry. The crystal structures of both [Ni(1,4-DMHEC-14)](ClO 4) 2 and [Ni(l,II-DMHEC14)](ClO 4) 2 have been determined by a combined molecular mechanics and X-ray crystallography study and show that in each isomer both pendant donors are coordinated in a trans-relationship, in addition to the four nitrogen atoms, giving rise to octahedral stereochemistry. In the former case the ligand is in the trans-III configuration whereas the latter complex has a trans-II geometry.

Chemical Ionization Mass Spectrometry of Bifunctional o-Xylylene Compounds. Absence of Proton Transfer Interactions between Two Functional Groups in Fragmenting Molecular Protonated Ions.

Chemical ionization mass spectra of bifunctional o-xylylene amino hydroxy derivatives were measured and compared to those of m- or p-compounds. The intensity of [MH]+ peaks from o-compounds were larger than those from m- or p-isomers. This is due to the stabilization by internal hydrogen bond formation between two neighboring functional groups in stable and non-decomposing [MH]+ ions. The extent of fragmentation ratio of each functional group was calculated from observed relative intensities of respective fragment ion peaks. Surprisingly the ratio falls into approximately the same range of the corresponding ratio of m- or p-compounds. The results indicated that internal hydrogen bond formation, which may lead to proton transfer, could not compete with the simple bond cleavage in energy-rich fragmenting [MH]+ ions.

Octanol/Water Partition Coefficient of Ortho-Substituted Aromatic Solutes

The partition coefficient (P) of some mono- and di-ortho- substituted aromatic compounds was measured in a 1-octanol/water system. For each series of compounds with the same functional group, the n-value (the difference in the log Rvalue between the substituted and unsubstituted compound) was analyzed on the same basis as the values of meta- and para-substituted isomers by an extended Hammett -Taft procedure. In the procedure, we considered the intramolecular electronic and steric effects, operating between substituents and governing the relative hydrogen-bonding solvation with partitioning solvents for solutes in which internal hydrogen-bond formation can be ignored. The TT value for mono- and di-ortho-substituted derivatives was adequately included in the correlation equation for the values of the meta- and para- substituted derivatives in each series. The effect of di-ortho substituents on partition behaviors could be roughly expressed by the sum of the effects of the 2- and 6-position substituents.

Polyphosphate chains by addition of oxiranes to phosphoric acid

Addition of diepoxides to the acids of phosphorus provides a new, attractive route to polyphosphates. In order to understand better the mechanism of this reaction and the structure of the products, the model reactions, namely additions of simple oxiranes to the acids of phosphorus, have been studied. It was shown that this reaction is catalysed by the P-OH groups of the acids. Activation of the oxirane molecule occurs predominantly by formation of the hydrogen bonded species while ionized form of acid plays only a minor role at the studied conditions (1,4-dioxane solution, 25°C). Reactivity of subsequent P-OH groups in phosphoric acid increases with increasing degree of substitution by -OCH2CH2OH groups. The ratio of the rate constants of formation of mono-, di-, and triesters of phosphoric acid is equal to 1/2/4. This has been attributed to the formation of internal hydrogen bonds, involving substituents and the P-OH groups. The observed order of the rate constants shows that reaction can not be stopped at the diester stage (linear units) and triester species (branched units) are formed fast. However, due to the large difference in the rate of hydrolysis, especially pronounced at basic conditions, triesters of phosphoric acid can easily be converted into the corresponding diesters by simple hydrolysis. Thus, the addition of diepoxides to phosphoric acid, followed by hydrolysis, leads to essentially linear polyphosphate chains.

The affinity and activity of compounds related to nicotine on the rectus abdominis muscle of the frog (Rana pipiens).

1. Series of pyridylalkyl- and substituted phenylalkyl-trimethylammonium salts, triethylammonium salts, diethylamines and di-n-propylamines have been made. The substituents in the benzene ring were nitro, chloro, bromo, methoxy, hydroxy and amino groups and the alkyl residues had one, two, or three methylene groups separating the aromatic nucleus from the cationic head.2. Most of the trimethylammonium compounds caused a contracture of the frog rectus muscle, but some were partial agonists and a few were antagonists. The di-n-propylamines were all antagonists, as were most of the diethylamines and triethylammonium compounds, though some of these were partial agonists and a few triethylammonium compounds were agonists. The affinities of the antagonists and partial agonists for the receptors stimulated by beta-pyridylmethyltrimethylammonium (and by nicotine) were measured. The equipotent molar ratios of all the agonists were measured relative to beta-pyridylmethyltrimethylammonium.3. The dissociation constants of the pyridylmethyldiethylamines and substituted benzyldiethylamines were measured. The effects of substituents on the pK(a) of benzyldiethylamine were similar to their effects on the pK(a) of aniline, though there were differences with some of the o-substituted compounds, which could be attributed to internal hydrogen-bond formation.4. There is no obvious correlation between the effects of a substituent on the pK(a) of benzyldiethylamine and its effects on affinity. Although increasing the size of the cationic group usually increased affinity, it did not always do so. The compounds with the highest affinity, p-hydroxybenzyldiethylamine (log K, 5.90) had about half the affinity of (+)-tubocurarine (log K, 6.11), but the triethylammonium analogue (log K, 4.17) had only about one-fiftieth of the affinity of the tertiary base. The binding of the drug to the receptor appears to involve many factors which include the size of the groups as well as their electron-releasing or withdrawing nature and other properties, such as their polar and lipophilic or lipophobic character.5. There is no obvious correlation between the effects of a substituent on the affinity of the diethylamino or triethylammonium compounds and its effects on the activity of the trimethylammonium analogue. The most active compounds contain hydroxy- and amino-, phenyl or beta-pyridyl groups, m-hydroxyphenyl-propyltrimethylammonium being about 50 times as active as nicotine, but the corresponding diethylamino or triethylammonium compounds do not have high affinity. There does not seem necessarily to be an inverse relationship between activity and affinity, however, because some m-nitro and m-chloro trimethylammonium compounds have considerable activity and the analogous triethylammonium compounds have considerable affinity.6. It is suggested that ability to activate these receptors is associated with the presence of substituents which can interact with water molecules which may be involved in the action of the drug at the receptor.