Fine grained sampling of residue characteristics using molecular dynamics simulation

In a fine-grained computational analysis of protein structure, we investigated the relationships between a residue's backbone conformations and its side-chain packing as well as conformations. To produce continuous distributions in high resolution, we ran molecular dynamics simulations over a set of protein folds (dynameome). In effect, the dynameome dataset samples not only the states well represented in the PDB but also the known states that are not well represented in the structural database. In our analysis, we characterized the mutual influence among the backbone ?,ψ angles with the first side-chain torsion angles (χ₁) and the volumes occupied by the side-chains. The dependencies of these relationships on side-chain environment and amino acids are further explored. We found that residue volumes exhibit dependency on backbone 2° structure conformation: side-chains pack more densely in extended β-sheet than in α-helical structures. As expected, residue volumes on the protein surface were larger than those in the interior. The first side-chain torsion angles are found to be dependent on the backbone conformations in agreement with previous studies, but the dynameome dataset provides higher resolution of rotamer preferences based on the backbone conformation. All three gauche^?, gauche⁺, and trans rotamers show different patterns of ?,ψ dependency, and variations in χ₁ value are skewed from their canonical values to relieve the steric strains. By demonstrating the utility of dynameomic modeling on the native state ensemble, this study reveals details of the interplay among backbone conformations, residue volumes and side-chain conformations.     

Synthesis of novel multi-arm star azobenzene side-chain liquid crystalline copolymers with a hyperbranched core

A series of novel multi-arm star side-chain liquid crystalline (LC) copolymers with hyperbranched core moieties were synthesized by atom transfer radical polymerization (ATRP) using a multi-functional hyperbranched polyether as the initiator and chlorobenzene as the solvent. The multi-functional hyperbranched polyether initiator was prepared from poly(3-ethyl-3-(hydroxymethyl)oxetane) (PEHO) and 2-bromo-2-methylpropionyl bromide. The azobenzene side-chain liquid crystalline arms were designed to have an LC conformation of poly[6-(4-methoxy-4^′-oxy-azobenzene)hexyl methacrylate] with different molecular weights. Their characterization was performed with ¹H NMR, size exclusion chromatograph (SEC), differential scanning calorimetry (DSC) and thermal polarized optical microscopy (POM). The multi-arm star side-chain liquid crystalline copolymers exhibited a smectic and a nematic phase, and the phase transition temperatures from the smectic to the nematic phase and from the nematic to isotropic phase increased with increasing the molecular weight of the multi-arm star side-chain liquid crystalline copolymers from 1.78 × 10⁴ to 9.07 × 10⁴.     

NMR Conformational Study of Aminoalkylbenzamides,Aminoalkyl-o-anisamides,and Metoclopramide,a Dopamine Receptor Antagonist

The conformational behaviour of metoclopramide, a neuroleptic benzamide, and model compounds was investigated byt ¹ H-NMR spectroscopy. An intramolecular amide-methoxy H-bond is shown to exist in CDCl₃-solution, but not in D₂O-solution, independently of the length and protonation state of the basic side-chain. This H-bond creates a virtual cycle which may be a key feature for the binding of neuroleptic benzamides to the dopamine receptor. The conformational behaviour of the aminoethyl side-chain is shown to be markedly condition-dependent. For metoclopramide and its analogues in their protonated form, the gauche- and trans- rotamers have identical energies in D₂O-as well as in CDCl₃-solutins. For the non-protonated molecules, the trans-rotamer is favoured in D₂O-solutin, while the gauche-rotamer is favoured in CDCl₃-solution (ΔG°?|0.5|kcal/mol in both cases). The side-chain conformation of neuroleptic benzamides is discussed in terms of receptor affinity.     

An Unusual Rearrangement during the Oxidative Addition of Hexafluoroacetone and Trifluoroacetophenone to 2-Bornanylen(dimethylphosphino)methyl Imine: Formation of a P=C Double Bond

The reaction of aminomethyl dimethylphosphine oxide and (1 R)–(+)-camphor furnished the σ⁴λ⁵-P Schiff base 1 . Reduction of 1 with trichlorosilane, followed by alkaline hydrolysis, led to 2-bornanylen(dimethylphosphino)methyl imine 2 . The 1,2-σ⁵λ⁵oxaphosphetane 5 , formed in the reaction of 2 with hexafluoroacetone, spontaneously rearranged into the P=C doubly bonded compound 9 at room temperature. Likewise, by oxidative addition of trifluoroacetophenone to 2 at 70 °C, 10 was formed. Compound 1 was subjected to an X-ray crystal structure analysis; the two independent molecules differ in the side-chain conformation.     

Thiocyclosporins: Preparation,Solution and Crystal Structure,and Immunosuppressive Activity

The reaction of cyclosporin A (CsA) with Lawesson's reagent under different conditions yields various thiocyclosporins, in which carbonyl O-atoms and/or the hydroxy O-atom of the MeBmt residue are replaced by an S-atom. The position of the S-atom is determined by NMR spectroscopy, and the conformations of the products are studied by NMR spectroscopy and X-ray crystallography. Some of the thiocyclosporins show interesting conformational properties. Whereas one conformation strongly dominates for CsA in CDCL₃, two conformers A and B, in a ratio 58:42 are found for [¹ψ², CS–NH]CsA. Extensive NMR studies including new 2D and 3D heteronuclear techniques and restrained MD calculations using ROE effects demonstrate that the major conformer A is identical to CsA, while the minor conformer B contains an additional cis peptide bond between the Sar³ and MeLeu⁴ residues. [⁴ψ⁵, CS? NH; ⁷ψ⁸, CS–NH]CsA exhibits a conformation very similar to crystalline CsA. However, the D-Ala⁸NH, MeLeu⁶Co γ-turn H-bond is not present in this dithio analogue. Also different is the MeBmt¹side-chain conformation, the dithio conformation showing a strong MeBmt¹OH, Sar³CO H-bond. Immunosuppressive activities of thiocyclosporins are measured in IL-2 and IL-8 reporter gene assays. Their activities are discussed in relation to their conformations.     

Discovering New Classes of <Emphasis Type="Italic">Brugia malayi</Emphasis> Asparaginyl-tRNA Synthetase Inhibitors and Relating Specificity to Conformational Change

SLIDE software, which models the flexibility of protein and ligand side chains while docking, was used to screen several large databases to identify inhibitors of Brugia malayi asparaginyl-tRNA synthetase (AsnRS), a target for anti-parasitic drug design. Seven classes of compounds identified by SLIDE were confirmed as micromolar inhibitors of the enzyme. Analogs of one of these classes of inhibitors, the long side-chain variolins, cannot bind to the adenosyl pocket of the closed conformation of AsnRS due to steric clashes, though the short side-chain variolins identified by SLIDE␣apparently bind isosterically with adenosine. We hypothesized that an open conformation of the motif 2 loop also permits the long side-chain variolins to bind in the adenosine pocket and that their selectivity for Brugia relative to human AsnRS can be explained by differences in the sequence and conformation of this loop. Loop flexibility sampling using Rigidity Optimized Conformational Kinetics (ROCK) confirms this possibility, while scoring of the relative affinities of the different ligands by SLIDE correlates well with the compounds’ ranks in inhibition assays. Combining ROCK and SLIDE provides a promising approach for exploiting conformational flexibility in structure-based screening and design of species selective inhibitors.     

NMR of some benzodiazepine drugs: Structure elucidation with lanthanide-induced shifts of N-1 substituted benzodiazepinones

Two 1,4-benzodiazepinones of psychopharmacological interest, pinazepam (2) and prazepam (3), were studied in solution by ¹³C and ¹H NMR. ¹H variable-temperature experiments showed that the seven-membered ring exists in a simple pseudo-boat form at room temperature, but the energy barrier is higher in 3 (ΔG_405°c = 82.8 kJ mol^?1) than in diazepam (1). Moreover, upon addition of LSR, the boat conformation is retained in the lanthanide ion-substrate complex, as with 1 in the solid state. Using a concentration-dependent shift technique and a computer-assisted LIS method, the conformations of the N-branched side-chain were investigated. Two preferred orientations were found for the propargyl group of 2, while three unequally populated conformations of the cyclopropyl moiety of 3 are distributed preferentially in the sterically unhindered space around the complex.     

INVESTIGATION OF LIGHT-INDUCED CONFORMATION CHANGES IN SPIROPYRAN-MODIFIED SUCCINYLATED POLY(l-LYSINE)

Abstract— To determine the maximum range of coupling between side-chain photochromism and polypeptide conformation change, we modified the carboxylate side chains of succinylated poly(l -lysine) with a spiropyran to form polypeptide I. The extent of modification was determined to be 35.5%. The spacer group length between the polypeptide a-carbon and the dye was 12 atoms, providing minimum polypeptide-dye interaction. Conformation changes were monitored by circular dichroism as a function of light adaptation and solvent composition (hexafluoroisopropanol [HFIP] vs trifluoroethanol [TFE]). Under all solvent compositions, the dark-adapted dye was in the merocyanine form. Light adaptation by visible light converted the dye to the spiropyran form. When dissolved in TFE, I adopted a helical conformation insensitive to light adaptation. With increasing percentage HFIP, a solvent-induced helix-to-coil transition was observed around 80% (vol/vol) HFIP. At 100% HFIP, both light- and dark-adapted forms of I were in the coil state. Near the midpoint of the solvent-induced helix-to-coil transition, light adaptation caused conformation changes. Applying helix-to-coil transition theory, we measured a statistically significant difference in coil segment-HFIP binding constant for light- v.v dark-adapted solutions (6.38 ± 0.03 M^-1vs 6.56 ± 0.03 M^-1), but not for the nucleation parameter σ (1.2 ± 0.4 10^-3 v.v 1.3 ± 0.3 × 10^-3). The small binding constant difference translated to a light-induced binding energy difference of 17 cal/mol/monomer. Near the midpoint of the helix-to-coil transition, collective interactions between monomer units made possible the translation of a small energy difference (less than RT) into large macromolecular conformation changes. This work parallels similar behavior observed in poly(isocyanate) (Green, M. M. et al. J. Am. Chem. Soc. 115 , 4941–4942, 1993). The subtle differences in dye-backbone interaction in I suggested a maximum coupling distance (12 atoms) beyond which polypeptide conformation and dye state are uncoupled.     

Dehydration of peptide [M + H]+ ions in the gas phase

The loss of water from protonated peptides was studied using [¹⁸O]-labeling of the C-terminal carboxyl group. The structures (including the location of the isotopic label) of first-generation product ions were examined by sequential product ion scanning (MS³ and MS⁴) using a hybrid sector/quadrupole mass spectrometer. Water loss may involve carboxylic acid groups, side-chain hydroxyls, or peptide backbone oxygens. Although one of these three pathways often predominates, more than one dehydration route can be operative for a single peptide structure. When peptide backbone oxygen is lost, the dehydration can occur at one or two primary sites along the backbone, with the location of the site(s) varying among peptides. When water loss involves the C-terminal carboxyl group, the resulting ion may undergo extensive intraionic oxygen isotope exchange. This evidence for complex intraionic interactions further emphasizes the significance of gas-phase conformation in determining the fragmentations of peptide ions.     

Mass spectrometry of aralkyl compounds with a functional group—XII: Unorthodox elimination of hydrogen cyanide from hydrogen randomized molecular ions of benzylcyanide and of o-, m- and p-cyanobenzylcyanides,revealed by D-, 13C- acid 15N-labelling

Specific D-labelling in the side-chain and in the phenyl ring, ¹³C-labelling in the benzylic position and in the cyano group and ¹⁵N-labelling in the cyano group of benzylcyanide show, that the molecular ion, decomposing in the second field free region, i.e. having a low internal energy, loses hydrogen cyanide with participation of both side-chain carbon atoms (22% benzylic carbon and 78% cyano carbon) after a complete randomization of all hydrogens. This sharply contrasts with the loss of hydrogen cyanide from the hydrogen randomized molecular ion, decomposing in the ion source, where the original cyano group is involved exclusively. The molecular ions of (o, m, p)-cyanobenzylcyanides, decomposing in the ion source as well as in the second field free region, also lose hydrogen cyanide, involving to some extent (6 to 15%) a carbon atom, different from that of the side-chain cyano group, after an extensive randomization of hydrogens as shown by specific D-labelling in several positions and by ¹³C- and ¹⁵N-labelling in the side-chain cyano group. Furthermore, the molecule of hydrogen cyanide, eliminated in the ion source and in the second field free region, appears to contain predominantly the side-chain cyano group (±70%), thus suggesting that few or none of the molecular ions have rearranged to a seven membered ring.     

A new method for side-chain conformation prediction using a Hopfield network and reproduced rotamers

We present a new side-chain prediction method based on energy minimization using a Hopfield network, focusing on the buried residues of proteins. In this method, the network is composed of automata assigned to each rotamer to restrict side-chain conformational space. We reproduced a rotamer library that enabled us to more widely cover the space for side-chain conformations than those previously produced. The accuracy of the side-chain modeling was estimated by three standards: root mean square deviations (rmsds) between the modeled and the crystal structures, the percentages of correctly predicted side-chain torsion angles, and the percentages of correctly predicted hydrogen bonds. The average rmsd for buried side chains of 21 proteins was 1.10 Å. The value was almost always improved relative to the previous works. The percentage of side-chain X₁ angles for buried residues was 87.3%. By considering the hydrogen bond energy, the average percentage of correctly predicted hydrogen bonds rose from 33% without hydrogen bond energy to 52% with the bond energy. We applied this method to homology modeling, where the protein backbone used to predict side-chain conformations deviates from the correct conformation, and could predict side-chain conformations as correctly as those using the correct backbones. © 1996 by John Wiley & Sons, Inc.     

Ab initio calculations on Pro-Ala and Pro-Gly dipeptides

The geometries of the dipeptides -Pro- -Ala, -Pro- -Ala and -Pro-Gly were investigated by a grid scan ab initio calculation. The 6-31G basis set was used to estimate the effect of the alanyl side-chain on the conformation of the peptide backbone and to provide a computational basis for the interpretation of known physical-chemical properties of larger peptides that contain these dipeptides. These calculations furnish a direct quantum mechanical assessment of the energetic consequences of a methyl side-chain in the i + 2 position of a turn. The results of the calculation support the current view that the presence of a -Ala residue in the i + 2 position favors a type II β-turn over a type I β-turn conformation, while -Ala has the opposite effect. Total and relative energies for all the optimized conformations identified by the grid search are given and geometric parameters (bond lengths, bond angles and dihedral angles) and net atomic charges have been calculated.     

Dynamic stereochemistry of imines and derivatives: 15—Carbon-13 NMR studies of aryl-substituted imines and oxaziridines

¹³C chemical shifts for several series of cis- and trans-N-alkylimines and oxaziridines bearing para-substituted C-phenyl rings are reported and correlated with dual substituent parameters. The ¹³C?N and oxaziridine ring carbon shifts correlate primarily with the inductive/field parameters, σ₁, whereas both resonance and inductive terms generally contribute about equally to the long-range substituent effects on alkyl side-chain chemical shifts. Correlations on diastereoisomeric imines show that the transmission of substituent effects can be significantly affected by the E–Z configuration. Aromatic carbon chemical shifts in imines are discussed in relation to the E–Z configuration and the conformation around the aryl—imino bond.     

Fast side-chain losses in keV ion-induced dissociation of protonated peptides

In this paper, we compare ionization and dissociation of a series of singly and doubly protonated peptides, namely leucine enkephalin, bradykinin, LHRH and substance P as induced by collisions with keV H⁺, He⁺ and He²⁺. For all peptides under study, the fragmentation pattern depends strongly on the electronic structure of the projectile ions. Immonium ions, side-chains and their fragments dominate the spectrum whereas fragments due to peptide backbone cleavage are weak or even almost absent for He⁺. Here, resonant electron capture from the peptide is ruled out and only interaction channels accompanied by much higher excitation contribute. Cleavage of the side-chain linkage appears to be a process alternative to backbone fragmentation occurring after internal vibrational redistribution of excitation energy. Depending on the peptide, this process can lead to the loss of a side-chain cation (leucine enkephalin, LHRH) or a neutral side-chain (substance P).     

Arginine Side-Chain Hydrogen Exchange: Quantifying Arginine Side-Chain Interactions in Solution

The rate with which labile backbone hydrogen atoms in proteins exchange with the solvent has long been used to probe protein interactions in aqueous solutions. Arginine, an essential amino acid found in many interaction interfaces, is capable of an impressive range of interactions via its guanidinium group. The hydrogen exchange rate of the guanidinium hydrogens therefore becomes an important measure to quantify side-chain interactions. Herein we present an NMR method to quantify the hydrogen exchange rates of arginine side-chain ¹H^ϵ protons and thus present a method to gauge the strength of arginine side-chain interactions. The method employs ¹³C-detection and the one-bond deuterium isotope shift observed for ¹⁵N^ϵ to generate two exchanging species in ¹H₂O/²H₂O mixtures. An application to the protein T4 Lysozyme is shown, where protection factors calculated from the obtained exchange rates correlate well with the interactions observed in the crystal structure. The methodology presented provides an important step towards characterising interactions of arginine side-chains in enzymes, in phase separation, and in protein interaction interfaces in general.     

Conformational studies of poly(cis-5-ethyl-D-proline)

Two possible conformations for poly(cis-5-ethyl-D -proline) have been identified and characterized by using combinations of ¹H- and ¹³C-NMR, CD, and ORD spectroscopic techniques. Both forms have helical conformations similar to those of poly(L -proline) characterized by different amide bonds (cis and trans). However, the carbonyl group of the amide in poly(cis-5-ethyl-D -proline) form II (trans) seems to be closer to perpendicular orientation with respect to the helical axis than in poly(L -proline) form II. The pyrrolidine ring conformation of form I (cis) is probably β⁺γ^?-puckered, whereas for form II it is probably β⁺-puckered in nature. The side-chain ethyl groups prefer to adopt anti conformations to the C₅? H bond, or prefer to have χ = 180°, regardless which of the two forms poly(cis-5-ethyl-D -proline) may like to assume. The experimental results agree well with our previous theoretical conformational energy calculations.     

Order in poly(N-(10-n-alkyloxycarbonyl-n-decyl)-maleimides)

Wide-angle and small-angle x-ray diffraction patterns of 11 poly(N-(10-n-alkyloxycarbonyl-n-decyl)maleimides) (PEMI) (including only even members of the series) have been obtained on unoriented samples. They show major maxima at two diffraction angles. The one at the larger angles is due to the interaction of neighboring n-alkyl side-chains. The smaller one (which shows second and third orders of diffraction in higher members of the series, n = 14 to n = 22, where n is the number of methylene groups in the external n-alkyl sequence in the side chain) is related to the distance between lamellar planes formed by the main chains. In all cases, the measured layer separation d_i is higher than the structural unit length L of the side-chain in the most extended conformation, and lower than the length corresponding to two side-chains. On the basis of the experimental results reported here, a model is proposed for the packing of these comblike polymers in the solid state. The mode of packing is also supported by infrared spectra in the 720 cm^?1 region for the ? CH₂? rocking mode of vibration of the n-alkyl side-chain.     

Water-Soluble Polymers with Appending Porphyrins as Bioinspired Catalysts for the Hydrogen Evolution Reaction

Molecular design to improve catalyst performance is significant but challenging. In enzymes, residue groups that are close to reaction centers play critical roles in regulating activities. Using this bioinspired strategy, three water-soluble polymers were designed with appending Co porphyrins and different side-chain groups to mimic enzyme reaction centers and activity-controlling residue groups, respectively. With these polymers, high hydrogen evolution efficiency was achieved in neutral aqueous media for electro- (turnover frequency >2.3×10⁴ s⁻¹) and photocatalysis (turnover number >2.7×10⁴). Porphyrin units are surrounded and protected by polymer chains, and more importantly, the activity can be tuned with different side-chain groups. Therefore, instead of revising molecular structures that is difficult from both design and synthesis points of view, polymers can be used to improve molecular solubility and stability and simultaneously regulate activity by using side-chain groups.     

Hydrophobic side-chain interactions in a family of dimeric amide foldamers-potential alpha-helix mimetics

A series of new alpha-helix mimetics based on a benzamide scaffold and potentially able to disrupt protein-protein interactions have been synthesized and characterized by X-ray analysis. Inspection of the solid state structures of aromatic amide dimers confirmed that the molecules adopt a curved conformation with intramolecular H-bonding between the amide NH and the alkoxy oxygen of the neighboring aromatic fragment (d_NH…_O ∼ 2 Å). Adjacent dimer molecules are prone to form supramolecular assemblies due to both hydrophobic alkyl side-chain/side-chain interactions and intermolecular H-bonding.     

Tuning thermal gelling behavior of <Emphasis Type="Italic">N</Emphasis>-isopropylacrylamide based copolymer through introducing cucurbit[8]uril ternary complex on side-chain

Thermo-gelation polymers have attracted increasing attention over decades. However, rare facile tuning method of sol-gel transition temperature restricted the wider application. Preceding study indicated that supramolecular interactions demonstrated a powerful means to control the structure and property of polymeric materials. Here we designed an N-isopropylacrylamide (NIPAM) based thermo-sensitive copolymer with naphthyl (Np) on its side chain. Positive-charged side-chain ternary complex was formed with cucurbit[8]uril (CB[8]) and methylviologen (MV²⁺) via CB[8]-enhanced intermolecular charge-transfer (CT) interaction. Introducing the ternary complex CB[8]/MV²⁺/Np on side-chain altered microstructure of macromolecular chains and led to a strong tendency for thermo gelation. Altering content of CB[8] and MV²⁺ changed content of the positive-charged side-chain ternary complex and varied gelation temperature. Therefore, introducing supramolecular interaction endowed the hydrogel with tunable gelation property.