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.     

Conformational analysis of allylamine. An ab initio molecular orbital study

The conformational characteristics of allylamine were investigated by the ab initio STO -3G basis set. The results indicate that the molecule exists in a number of stable conformations through rotations about the CC? NH and CC? CN bonds. The TE (trans-CCNLP , LP representing lone-pair electrons, and eclipsed-CCCH) is the most stable, while TC (trans-CCNLP and cis-CCCN), GE (gauche-CCNLP and eclipsed-CCCH), G′C(gauche′-CCNLP and cis-CCCN), and G′E (gauche′-CCNLP and eclipsed-CCCH) conformations are less stable, respectively, by 0.41, 0.67, 0.92, and 1.14 kcal mol^?1. These results are in general consistent with previous experimental results. Rationale for the conformational characteristics and order of stabilities are explored.     

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.     

α-Melanotropin Labelled at its Tyrosine2 Residue: Synthesis and Biological Activities of 3′-Iodotyrosine2-,3′-125Iodotyrosine2-,3′,5′-Diiodotyrosine2-, and (3′,5′-3H2)tyrosine2-α-Melanotropin,and of Related Peptides

α-MSH was labelled at its tyrosine² residue with tritium and iodine. Several synthetic routes were investigated by preparing 13 precursor or mode compounds and 4 different labelled products (via about 40 intermediates). Their melanotropic activity was determined with an in vitro frog skin assay and, for some of the compounds, with a tyrosinase assay. The tritiation was performed on [Tyr(I₂)²]α-MSH by catalytic halogen/tritium exchange, yielding α-MSH of high specific radioactivity (34 Ci/mmol) and full biological activity. Iodination was studied in detail using five different techniques. An equimolar chloramine T procedure proved to be the most convenient and reproducible method, resulting in monoiodinated α-MSH containing 99% of the label in position 2. The biological activity was 50% that of α-MSH; the specific radioactivity, determined in a competitive binding assay with a highly specific α-MSH antiserum and [Tyr(I)²]α-MSH as competitor, was 1530 Ci/mmol. The labelling techniques and the bioligical results are discussed.     

Three Types of Induced Tryptophan Optical Activity Compared in Model Dipeptides: Theory and Experiment

The tryptophan (Trp) aromatic residue in chiral matrices often exhibits a large optical activity and thus provides valuable structural information. However, it can also obscure spectral contributions from other peptide parts. To better understand the induced chirality, electronic circular dichroism (ECD), vibrational circular dichroism (VCD), and Raman optical activity (ROA) spectra of Trp‐containing cyclic dipeptides c‐(Trp‐X) (where X=Gly, Ala, Trp, Leu, nLeu, and Pro) are analyzed on the basis of experimental spectra and density functional theory (DFT) computations. The results provide valuable insight into the molecular conformational and spectroscopic behavior of Trp. Whereas the ECD is dominated by Trp π–π* transitions, VCD is dominated by the amide modes, well separated from minor Trp contributions. The ROA signal is the most complex. However, an ROA marker band at 1554 cm^?1 indicates the local χ₂ angle value in this residue, in accordance with previous theoretical predictions. The spectra and computations also indicate that the peptide ring is nonplanar, with a shallow potential so that the nonplanarity is primarily induced by the side chains. Dispersion‐corrected DFT calculations provide better results than plain DFT, but comparison with experiment suggests that they overestimate the stability of the folded conformers. Molecular dynamics simulations and NMR results also confirm a limited accuracy of the dispersion‐DFT model in nonaqueous solvents. Combination of chiral spectroscopies with theoretical analysis thus significantly enhances the information that can be obtained from the induced chirality of the Trp aromatic residue.     

Conformational Analysis of Fluorinated Pyrrolidines Using 19F–1H Scalar Couplings and Heteronuclear NOEs

A series of 3‐fluoropyrrolidines have been studied to investigate the influence of the stereoelectronic fluorine gauche effect on ring conformations in the solid state by single‐crystal X‐ray analysis and in solution phase by NMR spectroscopy. As part of these studies 1D ¹⁹F–¹H heteronuclear NOE (HOESY) experiments have been optimised for applications to small molecules and are described in detail. These have been employed to estimate ¹⁹F–¹H internuclear distances and were combined with vicinal ³J(F,H) and ³J(H,H) scalar coupling constants to analyse the ring conformations. Where possible the derived solution‐phase structural data have been compared with those of the crystalline state. The results demonstrate the influence of the gauche effect in stabilising C^γ‐exo conformations of the fluorinated pyrrolidines. It was further shown that when steric interactions were also present, this conformational bias was diminished and the contribution of the alternative C^γ‐endo conformation was seen to increase in solution at lower sample temperatures.     

Conformations of ethyl esters versus thiolesters

Ethyl formate and other substituted ethyl formates exist in stable anti and gauche conformations about the COCC dihedral angle, according to microwave spectroscopic studies. Similar studies of ethyl thiolformates characterize stable gauche conformations about the corresponding CSCC dihedral angle in every compound studied, but the anti conformation is found only in ethyl fluorothiolformate and chlorothiolformate. Ab initio calculations that include electron correlation via MP2 or the B3LYP density functional model have been carried out for ethyl and methyl formate and thiolformate and their fluoroformate analogs. These calculations reveal that the potential energy minima at gauche and anti COCC configurations are well developed in every case. However, although the gauche minimum for the CSCC torsional angle is clearly defined, the potential function near the anti CSCC configuration corresponds to a potential energy plateau rather than a minimum. In the case of ethyl fluorothiolformate, a modest well is predicted at the anti CSCC configuration, in agreement with experimental results. Received: 7 July 1998 / Accepted: 21 September 1998 / Published online: 15 February 1999     

Divergent Melanophore-Dispersing and Tyrosinase-Stimulating Activity of Synthetic Leucine9-α-melanotropin

Leucine⁹-α-melanotropin ([Leu⁹]α-MSH) was synthesized in homogeneous solution by a fragment condensation approach, and it was assayed for its melanophore-dispersing and its tyrosinase-stimulating activity with a reflectometric in vitro frog skin assay and with cultured mouse melanoma cells, respectively. In both assay systems, parallel log dose-response curves were obtained for ([Leu⁹)]α-MSH and α-MSH; however, in the frog skin assay the activity of the title compound was 1 middot; 10¹⁰ Units/mmol, i.e. 25% of the activity of α-MSH, whereas its tyrosinasestimulating potency was only 1% compared to α-MSH (EC₅₀= 2.5 · 10^?7M ). This indicates a major difference in the recognition/stimulation process of the receptors of the two cell types.     

The Influence of the Amino Acid Side Chains on the Raman Optical Activity Spectra of Proteins

The Raman optical activity (ROA) spectra of proteins show distinct patterns arising from the secondary structure. It is generally believed that the spectral contributions of the side-chains largely cancel out because of their flexibility and the occurrence of many side-chains with different conformations. Yet, the influence of the side-chains on the ROA patterns assigned to different secondary structures is unknown. Here, the first systematic study of the influence of all amino acid side-chains on the ROA patterns is presented based on density functional theory (DFT) calculations of an extensive collection of peptide models that include many different side-chain and secondary structure conformations. It was shown that the contributions of the side-chains to a large extent average out with conformational flexibility. However, specific side-chain conformations can have significant contributions to the ROA patterns. It was also shown that α-helical structure is very sensitive to both the exact backbone conformation and the side-chain conformation. Side-chains with χ₁≈−60° generate ROA patterns alike those in experiment. Aromatic side-chains strongly influence the amide III ROA patterns. Because of the huge structural sensitivity of ROA, the spectral patterns of proteins arise from extensive conformational averaging of both the backbone and the side-chains. The averaging results in the fine spectral details and relative intensity differences observed in experimental spectra.     

Effect of pH on the rotational conformations of 1,3‐diamino‐2‐hydroxypropane

The effect of pH on the rotational conformations of 1,3‐diamino‐2‐hydroxypropane in aqueous solution was investigated by proton NMR. Both the observed chemical shifts and coupling constants were used to calculate experimental pK_a values. The observed couplings were correlated with the expected couplings for the various possible staggered conformations to try to determine the pattern of conformations for the diamine and its conjugate acids. The best fits suggested a modest preference for the gauche–gauche conformation, especially at low pH, where the diprotonated hydroxydiamine predominates. In methanol, dimethyl sulfoxide and trichloromethane solutions, it was only possible to evaluate the conformational equilibria of the diamine. Slow proton exchange, which caused uncertainties in both chemical shifts and couplings for the monoprotonated and unprotonated diamine, nullified efforts to determine whether or not hydrogen bonding was important for these species in less polar solvents. Copyright © 2002 John Wiley & Sons, Ltd.     

Synthesis and Conformational Analysis of Hybrid α/β‐Dipeptides Incorporating S‐Glycosyl‐β2,2‐Amino Acids

We synthesized and carried out the conformational analysis of several hybrid dipeptides consisting of an α‐amino acid attached to a quaternary glyco‐β‐amino acid. In particular, we combined a S‐glycosylated β^2,2‐amino acid and two different types of α‐amino acid, namely, aliphatic (alanine) and aromatic (phenylalanine and tryptophan) in the sequence of hybrid α/β‐dipeptides. The key step in the synthesis involved the ring‐opening reaction of a chiral cyclic sulfamidate, inserted in the peptidic sequence, with a sulfur‐containing nucleophile by using 1‐thio‐β‐D ‐glucopyranose derivatives. This reaction of glycosylation occurred with inversion of configuration at the quaternary center. The conformational behavior in aqueous solution of the peptide backbone and the glycosidic linkage for all synthesized hybrid glycopeptides was analyzed by using a protocol that combined NMR experiments and molecular dynamics with time‐averaged restraints (MD‐tar). Interestingly, the presence of the sulfur heteroatom at the quaternary center of the β‐amino acid induced θ torsional angles close to 180° (anti). Notably, this value changed to 60° (gauche) when the peptidic sequence displayed aromatic α‐amino acids due to the presence of CH–π interactions between the phenyl or indole ring and the methyl groups of the β‐amino acid unit.     

Influence of Side Chain Conformation on the Activity of Glycosidase Inhibitors

Substrate side chain conformation impacts reactivity during glycosylation and glycoside hydrolysis and is restricted by many glycosidases and glycosyltransferases during catalysis. We show that the side chains of gluco and manno iminosugars can be restricted to predominant conformations by strategic installation of a methyl group. Glycosidase inhibition studies reveal that iminosugars with the gauche,gauche side chain conformations are 6- to 10-fold more potent than isosteric compounds with the gauche,trans conformation; a manno-configured iminosugar with the gauche,gauche conformation is a 27-fold better inhibitor than 1-deoxymannojirimycin. The results are discussed in terms of the energetic benefits of preorganization, particularly when in synergy with favorable hydrophobic interactions. The demonstration that inhibitor side chain preorganization can favorably impact glycosidase inhibition paves the way for improved inhibitor design through conformational preorganization.     

Intrinsic energy landscapes of amino acid side-chains

Amino acid side-chain conformational properties influence the overall structural and dynamic properties of proteins and, therefore, their biological functions. In this study, quantum mechanical (QM) potential energy surfaces for the rotation of side-chain χ(1) and χ(2) torsions in dipeptides in the alphaR, beta, and alphaL backbone conformations were calculated. The QM energy surfaces provide a broad view of the intrinsic conformational properties of each amino acid side-chain. The extent to which intrinsic energetics dictates side-chain orientation was studied through comparisons of the QM energy surfaces with χ(1) and χ(2) free energy surfaces from probability distributions obtained from a survey of high resolution crystal structures. In general, the survey probability maxima are centered in minima of the QM surfaces as expected for sp(3) (or sp(2) for χ(2) of Asn, Phe, Trp, and Tyr) atom centers with strong variations between amino acids occurring in the energies of the minima indicating intrinsic differences in rotamer preferences. High correlations between the QM and survey data were found for hydrophobic side-chains except Met, suggesting minimal influence of the protein and solution environments on their conformational distributions. Conversely, low correlations for polar or charged side-chains indicate a dominant role of the environment in stabilizing conformations that are not intrinsically favored. Data also link the presence of off-rotamers in His and Trp to favorable interactions with the backbone. Results also suggest that the intrinsic energetics of the side-chains of Phe and Tyr may play important roles in protein folding and stability. Analyses on whether intrinsic side-chain energetics can influence backbone preference identified a strong correlation for residues in the alphaL backbone conformation. It is suggested that this correlation reflects the intrinsic instability of the alphaL backbone such that assumption of this backbone conformation is facilitated by intrinsically favorable side-chain conformations. Together our results offer a broad overview of the conformational properties of amino acid side-chains and the QM data may be used as target data for force field optimization.     

Folding and self-association of atTic20 in lipid membranes: implications for understanding protein transport across the inner envelope membrane of chloroplasts

Background

We have previously shown that the P. gingivalis HmuY hemophore-like protein binds heme and scavenges heme from host hemoproteins to further deliver it to the cognate heme receptor HmuR. The aim of this study was to characterize structural features of HmuY variants in the presence and absence of heme with respect to roles of tryptophan residues in conformational stability.

Results

HmuY possesses tryptophan residues at positions 51 and 73, which are conserved in HmuY homologs present in a variety of bacteria, and a tryptophan residue at position 161, which has been found only in HmuY identified in P. gingivalis strains. We expressed and purified the wildtype HmuY and its protein variants with single tryptophan residues replaced by alanine or tyrosine residues. All HmuY variants were subjected to thermal denaturation and fluorescence spectroscopy analyses. Replacement of the most buried W161 only moderately affects protein stability. The most profound effect of the lack of a large hydrophobic side chain in respect to thermal stability is observed for W73. Also replacement of the W51 exposed on the surface results in the greatest loss of protein stability and even the large aromatic side chain of a tyrosine residue has little potential to substitute this tryptophan residue. Heme binding leads to different exposure of the tryptophan residue at position 51 to the surface of the protein. Differences in structural stability of HmuY variants suggest the change of the tertiary structure of the protein upon heme binding.

Conclusions

Here we demonstrate differential roles of tryptophan residues in the protein conformational stability. We also propose different conformations of apo- and holoHmuY caused by tertiary changes which allow heme binding to the protein.     

Screening the thermal stability of carotenoids-α lactalbumin complex by spectroscopic and molecular modeling approach

Sea buckthorn is a natural food ingredient rich in carotenoids, tocopherols, sterols, flavonoids, lipids, vitamins, tannins and minerals. In this study, we investigated the themostability of the complex formed between α-lactalbumin (α-LA) with carotenoids from sea buckthorn berries extract (CSB) in the temperature range of 25°C to 100°C. The heat induced conformational changes of the α-LA-CSB complex were studied by using fluorescence and molecular modeling techniques. Phase diagram indicated the presence of more than one structurally distinct species as an indicator that temperature influenced the conformation of α-LA. Intrinsic fluorescence studies revealed that carotenoids trapped into the core of α-LA do not bind in locations close to tryptophan (Trp) residues. The synchronous spectra indicated that the interaction between α-LA and CSB had no apparent influence on the local conformation of Trp and tyrosine (Tyr) microenvironments within protein structure. Quenching studies with acrylamide showed that Trp residues had the highest exposure at 80°C, being least accessible to quencher at 60°C. In agreement with the fluorescence spectroscopy observations, the in silico analysis at single molecules level indicated a significant increase of 46.42 Å² and 80.07 Å² of the total accessible surface area of Trp and Tyr residues, respectively with the temperature increase from 25°C to 90°C. Concerning the thermodynamic properties of the α-LA-β-carotene model, the molecular modeling results indicate that the thermal treatment is not favorable for preserving the stability of the complex.     

Membrane Structure of Substance P. II. Secondary Structure of Substance P, [9-Leucine]substance P,and Shorter Segments in 2,2,2-Trifluoroethanol,Methanol, and on Liposomes Studied by Circular Dichroism

Comparative CD studies with substance P ( 1 ), [Leu⁹]substance P ([Leu⁹]- 1 ), and their shorter peptide segments supported the membrane structures predicted for substance P and [Leu⁹]substance P. They indicated that the C-terminal segments (from residue 3 or 4 onward) can adopt α-helical conformations in hydrophobic environments and on lipid membranes. The N-terminal segment, (residues 1–4) had a poly(proline)-like conformation in aqueous and hydrophobic surroundings. Residues 3 and 4 (Lys-Pro) appeared to belong to both domains and bring about the transition between the two. The estimated free energies of transfer for 1 and [Leu⁹]- 1 from their random conformations in H₂O to their partially helical conformations on an aqueous-hydrophobic interface are too small to allow detectable interaction with neutral lipid membranes at low concentrations. The two peptides should, however, interact detectably with anionic membranes because of favourable Boltzmann distribution factors. This prediction was shown to be correct for liposomes prepared from 1,2-dioleoyl-sn-glycero-3-phosphocholine (neutral) and phosphatidylserine (anionic).     

Chemical Synthesis and Biological Activity of the Dogfish (Squalus acanthias) α-melanotropins I and II,and of related peptides

The purpose of this investigation is to provide synthetic proof for the structure of dogfish (Squalus acanthias) α-MSH and to investigate the consequences of the presence of methionine in position 13 and the lack of the N-terminal acetyl group in this hormone. Because of the facile oxidation of methionine (13) during handling or storage, a number of specifically oxidized hormones (Met⁴ and Met¹³) as well as tripeptides belonging to the C-terminal second message sequence were investigated. All the products were prepared by classical methods in homogeneous solution; intermediate and end products were extensively purified and characterized (Tables 3 and 4). The assays for melanotropic activity were performed in vitro with the modified reflectometric assay using the skin of Rana pipiens. It is concluded that the structures assigned to dogfish α-MSH I and II are correct and that the isolated samples contain slight quantities of [13-methionine (S-oxide)]dogfish α-MSH and [4, 13-bis-methionine (S-oxide)]dogfish α-MSH. The peptides with methionine in position 13 are as active in this assay as those containing valine. This also holds for the ? NH₂/? OH interchange distinguishing dogfish α-MSH I from dogfish α-MSH II. However, the lack of the N-terminal acetyl group strongly reduces the biological activity. Its introduction into dogfish α-MSH I results in a product that is equipotent with mammalian α-MSH. These and other conclusions are discussed in detail.     

Energetics of Stretching of Conformational Defects in Extended Poly(methylene) Chains

The deformation energetics of highly extended poly(methylene) segments with conformational defects of the kink and jog types, is investigated by molecular mechanics calculations. The deformation potential displays abrupt discontinuities as a result of sudden gauche‐to‐trans conformational transitions accompanied by a release of the elastic energy stored in all valence parameters. By stretching, the chain defects are sequentially annihilated, with the weakest elements interconverting first. Due to sudden drops in force the calculated force–length curves F(R) display a sawtooth‐like profile. The force jumps define a maximum load F_c that defect chains can bear prior to conformational “yielding”. The F_c in the range about 0.7–1.1 nN is found in highly extended multikink chains. The results suggest that the sawtooth‐like profile can be a common feature of mechanochemistry of bridging polymers with the restricted number of available conformations. A similar pattern of F(R) curves were previously observed at stretching and sequential unfolding of compact structural domains in biomacromolecules. Further, the calculations predict a distinct reduction of the longitudinal Young's modulus E with increasing concentration of kinks in molecules.     

Peptide models XVI. The identification of selected HCO—L—SER—NH2 conformers via a systematic grid search using ab initio potential energy surfaces

Multidimensional conformational analysis (MDCA) predicted the existence of nine stable backbone conformations (α_L, α_D, β_L, γ_L, γ_D, δ_L, δ_D, ϵ_L, and ϵ_D) on the 2D-Ramachandran map, E = E(ϕ, ψ), for a single amino acid diamide (HCONH-CHR-CONH₂). The potential energy hypersurfaces (E = E[ϕ, ψ, χ₁, χ₂]) of For-L-Ser-NH₂ associated with the α_L-, bgr;_L-, γ_L-, δ_L-, and ϵ_L-type stable backbone orientations are investigated in this article. An appropriate number of side-chain rotamers is associated with each of the backbone conformers. In the case of serine, where R = −CH₂OH, the two sidechain torsional angles (χ₁, χ₂) should lead to 3 * 3 = 9 different sidechain orientations according to MDCA. For certain backbone structures, some of the sidechain conformations were nonexistent. © 1996 by John Wiley & Sons, Inc.     

INTERACTION OF THE PEPTIDE HORMONE ADRENOCORTICOTROPIC ACTH(l-24), WITH A MEMBRANE MODEL SYSTEM: A FLUORESCENCE STUDY*

The peptide hormone adrenocorticotropin and a related peptide were studied in solution and in interaction with a model system of membranes (small unilamellar vesicles of dipalmitoylphosphatidylcholine and 17% dimyristoylphosphatidylglycerol) via fluorescence spectroscopy. In aqueous solution, intramolecular distances between the fluorescent residues R(Tyr²-Trp⁹) = 9.2 Å and R(Trp⁹-Tyr²³) 18 Å were obtained, in agreement with molecular models. Interaction of the peptide with the negatively charged membrane is evident from the alteration of the Trp photophysical parameters (quantum yield, fluorescence spectra and anisotropy), with a partition constant between the lipidic and aqueous phase of Kp =1–2 times 10³. The existence of two populations of Trp in the membrane, which are distinctly accessed by acrylamide, was concluded from the tryptophan fluorescence quenching study; the two fractions are located near the membrane interface as inferred from its fluorescence quenching by the 5-doxylstearate and 16-doxylstearate lipophilic quenchers. This result is further supported by energy transfer experiments to the 3-(9-anthroyloxyl)stearic acid and 12-(9-anthroyloxyl)stearic acid probes.