Chain Torsion Research Articles

Conformational analysis and vibrational spectroscopic investigation of L-alanyl-L-glutamine dipeptide

In this study conformational behavior of anticancer chemotherapy dipeptide Ala-Gln and its dimers have been investigated by molecular mechanic and ab-initio calculations. The calculations on Ala-Gln dipeptide as a function of side chain torsion angles, enable us to determine their energetically preferred conformations. The relative positions of the side chain residues of the stable conformations of dipeptide were obtained, depending on the obtained conformational analysis results. The lowest energy conformation of the dipeptide has been determined by using the Ramachandran maps (Biopolymers 6 (1963), 1494; J. Mol. Biol.7 (1963), 95) and compared with the quantum chemical ab-initio results. The geometry optimization, vibrational wavenumbers and intensity calculations of Ala-Gln dipeptide were carried out with the Gaussian03 program by using DFT with B3LYP functional and 6-31

Synthesis, spectroscopic and structural elucidation of 1-butyl-4-[2-(3,5-dimethoxy-4-hydroxyphenyl)ethenyl)]pyridinium chloride tetrahydrate

The novel chloride salt of 1-butyl-4-[2-(4-hydroxyphenyl)ethenyl)]pyridine ( 1), has been synthesized as the tetrahydrate and its structure and properties elucidated in detail spectroscopically, thermally and structurally, using single crystal X-ray diffraction, linear-polarized solid-state IR-spectroscopy, UV-spectroscopy and mass spectrometry. Quantum chemical calculations were performed with a view to supporting and explaining the experimental structural and spectroscopic data. The compound ( 1) crystallizes in triclinic P 1 ¯ space group and its unit cell contains two independent 1-butyl-4-[2-(3,5-dimethoxy4-hydroxyphenyl)ethenyl)]pyridinium] cations, differing with respect to the butyl chain torsion angle for which values of 80.0(9)° and 173.6(3)° are observed. The cations and anions are joined into infinite layers, formed by two different dimers and including solvent molecules. Hydrogen bonds OH⋯OH 2 (2.814 Å), HOH⋯O(CH 3) (2.960 Å), OH⋯Cl (2.967 Å), HOH⋯Cl − (3.034, 3.188, 3.161 and 3.062 Å) and HOH⋯OH 2 (2.772 Å) are observed. For first time in the literature, we are reporting the crystal structure of the dye with the syring-fragment in the molecule. The spectroscopic properties of the novel compound are compared and with those of the corresponding quinoide form ( 2). Both the forms ( 1) and ( 2) are characterized by 21 and 140 nm solvatochromic effects depending of the type of the solvent. The UV-spectroscopic data in solution confirm the formation of classical H-aggregates in polar protic solvent mixture.

Ethyl 2-acetyl-3-(4-chloroanilino)butanoate

The title compound, C14H18ClNO3, adopts an extended conformation, with all of the main chain torsion angles associated with the ester and amino groups trans. In the crystal, inversion dimers linked by pairs of N—H⋯O hydrogen bonds are observed.

The NMR Structures of the Major Intermediates of the Two-domain Tick Carboxypeptidase Inhibitor Reveal Symmetry in Its Folding and Unfolding Pathways

There is a lack of experimental structural information about folding intermediates of multidomain proteins. Tick carboxypeptidase inhibitor (TCI) is a small, disulfide-rich protein consisting of two domains that fold and unfold autonomously through the formation of two major intermediates, IIIa and IIIb. Each intermediate contains three native disulfide bonds in one domain and six free cysteines in the other domain. Here we have determined the NMR structures of these two intermediates trapped and isolated at acidic pH in which they are stable and compared their structures with that of the native protein analyzed under the same conditions. Both IIIa and IIIb were found to contain a folded region that corresponds to the N- and C-terminal domains of TCI, respectively, with structures very similar to the corresponding regions of the native protein. The remainder of the polypeptide chains of the intermediates was shown to be unfolded in a random coil conformation. Solvent exchange measurements further indicated that the two protein domains are not completely independent, but affect each other in terms of dynamics and stability, in agreement with reported inhibitory activity data. The derived results provide structural evidence for symmetric TCI folding and unfolding mechanisms that converge in IIIa and IIIb and reveal the structural basis that accounts for the strong and simultaneous accumulation of both intermediates. Altogether, this work has important implications for a better understanding of the folding mechanisms of multidomain, disulfide-rich proteins.

Citrullination-dependent Differential Presentation of a Self-peptide by HLA-B27 Subtypes

Inflammatory processes are accompanied by the posttranslational modification of certain arginine residues within proteins to yield citrulline, although it is largely unknown how this modification influences antigen presentation. We employed crystallographic and functional studies to investigate whether the exchange of arginine to citrulline affects the display of a peptide by two human major histocompatibility antigen class I subtypes, HLA-B(*)2705 and HLA-B(*)2709. Both differ only in residue 116 within the peptide binding groove despite their differential association with ankylosing spondylitis, an inflammatory rheumatic disorder. The crystal structures described here show that a modified self-peptide, pVIPR-U5 (RRKWURWHL; U = citrulline), is presented by the two HLA-B27 molecules in distinct conformations. These binding modes differ not only drastically from each other but also from the conformations exhibited by the non-citrullinated peptide in a given subtype. The differential reactivity of HLA-B27-restricted cytotoxic T cells with modified or unmodified pVIPR supports the structural findings and shows that the presentation of citrullinated peptides has the potential to influence immune responses.

FlexE ensemble docking approach to virtual screening for CDK2 inhibitors

In spite of a proven potential and effectiveness of FlexE in docking flexible ligands into an ensemble of protein structures, FlexE has rarely been successful in virtual screening situations. In this study, we constructed cyclin-dependent kinase 2 (CDK2) ensemble structures which have exactly the same backbone conformations as 1AQ1 but differ only at the side chain torsion angles of the key amino acid (Lys33, Phe80, Lys89 and Asp145) residues: the torsion angles observed in the 17 CDK2 crystal structures were adapted to represent conformational flexibility. FlexE ensemble docking protocol then completely samples the full conformational fields generated by combination of torsions of the four amino acids in the ATP binding site. Virtual screening for CDK2 inhibitors by using the FlexE ensemble docking of a database composed of 48,703 inactives and 82 actives showed significant enrichment factor (EF = 18.5), and successfully identified 71 actives among the top 132 ligands (53.8%) ranked by total energy scores. Moreover, total energy scoring followed by visual inspection filtered-off non-specific binders among the highly-ranked ligands to increase the ratio of actives-to-inactives to 71:13 at the top 5% of the virtual screening solutions.

MOLECULAR DYNAMICS STUDY OF ADSORPTION OF FLUORIC POLYMERS ON TATB SURFACE

Molecular dynamics simulation has been applied to study the adsorption process of PVDF/PCTFE copolymers on TATB (001) surfaces. The copolymers were formed by linking PVDF and PCTFE in 1:1 proportion as ABABAB pattern with the degree of polymerization N ranging from 10 to 200. The equilibrium time of each chain is several hundred picoseconds, and the adsorption energy E a increases with the distance H between the chain and the increased surface. Adsorption process occurs when H is below 10 Å, and E a tends to be zero as H becomes greater than 10 Å. Polymer's adsorbability is related to the length of the chain, and a longer chain is better than a short one. A short chain has more train conformation monomers than a long chain. Chain conformation changes greatly during the first hundred ps, and stabilizes after 150 ps. Monomers close to the TATB surface are easy to approach the surface, and the units far from the surface will approach the surface by chain torsion and bond rotation. The ratio of the number of train conformation monomers to the degree of polymerization N t /N increases with the increasing MD simulation time.

Steiner minimal trees, twist angles, and the protein folding problem

The Steiner Minimal Tree (SMT) problem determines the minimal length network for connecting a given set of vertices in three-dimensional space. SMTs have been shown to be useful in the geometric modeling and characterization of proteins. Even though the SMT problem is an NP-Hard Optimization problem, one can define planes within the amino acids that have a surprising regularity property for the twist angles of the planes. This angular property is quantified for all amino acids through the Steiner tree topology structure. The twist angle properties and other associated geometric properties unique for the remaining amino acids are documented in this paper. We also examine the relationship between the Steiner ratio rho and the torsion energy in amino acids with respect to the side chain torsion angle chi(1). The rho value is shown to be inversely proportional to the torsion energy. Hence, it should be a useful approximation to the potential energy function. Finally, the Steiner ratio is used to evaluate folded and misfolded protein structures. We examine all the native proteins and their decoys at http://dd.stanford.edu. and compare their Steiner ratio values. Because these decoy structures have been delicately misfolded, they look even more favorable than the native proteins from the potential energy viewpoint. However, the rho value of a decoy folded protein is shown to be much closer to the average value of an empirical Steiner ratio for each residue involved than that of the corresponding native one, so that we recognize the native folded structure more easily. The inverse relationship between the Steiner ratio and the energy level in the protein is shown to be a significant measure to distinguish native and decoy structures. These properties should be ultimately useful in the ab initio protein folding prediction.

Exploring the binding site of the human muscarinic M3 receptor: Homology modeling and docking study

AbstractThe human muscarinic M3 receptor (hM3) and its interactions with selective agonists and antagonists were investigated by means of combined homology and docking approach. Also, two pharmacophoric models for the hM3 agonist and antagonist binding sites were proposed. The three‐dimensional (3D) structure of hM3 receptor was modeled based on the high‐resolution X‐ray structure of bovine rhodopsin from the Protein Data Bank (PDB). To validate the reliability of the model obtained, the main chain torsion angles phi (Ψ) and psi (Φ) were examined in a Ramachandran plot, and all omega angles were measured for peptidic bond planarity. The characteristics of the active site, the position, and the orientation of ligands in situ, as well as the binding modes of the representative agonists and antagonists, were analyzed by applying a molecular docking technique using the AutoDock 3.0.5 program. Specific interactions responsible for recognition of the hM3 receptor, like ionic bond formed between protonated amine of the ligands and the Asp3.6 side chain were identified. Structure–reactivity relationships have been explained by analyzing the 3D structure of the hM3 model and the ligand conformations resulted from molecular docking simulation. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007

The Ig Doublet Z1Z2: A Model System for the Hybrid Analysis of Conformational Dynamics in Ig Tandems from Titin

Titin is a gigantic elastic filament that determines sarcomere ultrastructure and stretch response in vertebrate muscle. It folds into numerous Ig and FnIII domains connected in tandem. Data on interdomain arrangements and dynamics are essential for understanding the function of this filament. Here, we report a mechanistic analysis of the conformational dynamics of two Ig domains from the N terminus of titin, Z1Z2, by using X-ray crystallography, SAXS, NMR relaxation data, and residual dipolar couplings in combination. Z1Z2 preferentially adopts semiextended conformations in solution, with close-hinge arrangements representing low-probability states. Although interdomain contacts are not observed, the linker appears to acquire moderate rigidity via small, local hydrophobic interactions. Thus, Z1Z2 constitutes an adaptable modular system with restricted dynamics. We speculate that its preexistent conformation contributes to the selective recruitment of the binding partner telethonin onto the repetitive surface of the filament. The structural interconversion of four Z1Z2 conformers is analyzed.

Modeling the Absorption Spectrum of Tryptophan in Proteins

We have applied time-dependent density functional theory (TDDFT) to study the valence pi-pi* excited states of the tryptophan chromophore in the environment of the proteins barnase and human serum albumin. The chromophore is represented by indole. Due to the approximate nature of TDDFT, in the gas phase the calculated vertical transition energies to the 1L valence states are reordered with respect to experiment. The 1L(a) state responds more than the 1L(b) state to the local environment, described fully at the TDDFT level, and to bulk environment, described by a set of point charges. Nevertheless, the vertical transitions are readily identified. For human serum albumin, our calculations predict distinct spectral characteristics between structures with different tryptophan side chain torsion angles. The computational tractability of TDDFT relative to more accurate ab initio methods allows a large part of the surrounding protein environment (up to 100 atoms) to be explicitly included in the TDDFT calculations.

A Complete Set of NMR Chemical Shifts and Spin−Spin Coupling Constants forl-Alanyl-l-alanine Zwitterion and Analysis of Its Conformational Behavior

With the aid of labeling with stable isotopes ((15)N and (13)C) a complete set of chemical shifts and indirect spin-spin coupling constants was obtained for the zwitterionic form of L-alanyl-L-alanine in aqueous solution. Different sensitivities of the NMR parameters to the molecular geometry were discussed on the basis of comparison with ab initio (DFT) calculated values. An adiabatic two-dimensional vibrational wave function was constructed and used for determination of the main chain torsion angle dispersions and conformational averaging of the NMR shifts and coupling constants. The quantum description of the conformational dynamics based on the density functional theory and a polarizable continuum solvent model agrees reasonably with classical molecular dynamics simulations using explicit solvent. The results consistently evidence the presence of a single form in the aqueous solution with equilibrium main chain torsion angle values (psi = 147 degrees, varphi = -153 degrees), close to that one found previously in an X-ray study. Under normal temperature the torsion angles can vary by about 10 degrees around their equilibrium values, which leads, however, to minor corrections of the NMR parameters only. The main chain heavy atom chemical shifts and spin-spin coupling constants involving the alpha-carbon and hydrogen atoms appear to be most useful for the peptide structural predictions.

Chain Conformations and Photoluminescence of Poly(di-n-octylfluorene)

The diverse steady-state spectroscopic properties of poly(di-n-octylfluorene) are addressed from a molecular-level perspective. Modeling of representative oligomers support the experimental observation of at least three distinguishable classes of conformational isomers with differing chain torsion angles. One class appears to be populated by a single compact structural isomer, and this conforms to the so-called beta phase. A rigorous Franck-Condon analysis of the photoluminescence in conjunction with Frenkel-type exciton band structure calculations is performed. These results accurately reproduce all major spectral features of the photoabsorption and those of singlet exciton emission.

CORCEMA refinement of the bound ligand conformation within the protein binding pocket in reversibly forming weak complexes using STD-NMR intensities

We describe an intensity-restrained optimization procedure for refining approximate structures of ligands within the protein binding pockets using STD-NMR intensity data on reversibly forming weak complexes. In this approach, the global minimum for the bound-ligand conformation is obtained by a hybrid structure refinement method involving CORCEMA calculation of intensities and simulated annealing optimization of torsion angles of the bound ligand using STD-NMR intensities as experimental constraints and the NOE R-factor as the pseudo-energy function to be minimized. This method is illustrated using simulated STD data sets for typical carbohydrate and peptide ligands. Our procedure also allows for the optimization of side chain torsion angles of protein residues within the binding pocket. This procedure is useful in refining and improving initial models based on crystallography or computer docking or other algorithms to generate models for the bound ligand (e.g., a lead compound) within the protein binding pocket compatible with solution STD-NMR data. This method may facilitate structure-based drug design efforts.

The crystal structure of placental growth factor in complex with domain 2 of vascular endothelial growth factor receptor-1.

Placental growth factor (PlGF) is a member of the vascular endothelial growth factor (VEGF) family and plays an important role in pathological angiogenic events. PlGF exerts its biological activities through binding to VEGFR1, a receptor tyrosine kinase that consists of seven immunoglobulin-like domains in its extracellular portion. Here we report the crystal structure of PlGF bound to the second immunoglobulin-like domain of VEGFR1 at 2.5 A resolution and compare the complex to the closely related structure of VEGF bound to the same receptor domain. The two growth factors, PlGF and VEGF, share a sequence identity of approximately 50%. Despite this moderate sequence conservation, they bind to the same binding interface of VEGFR1 in a very similar fashion, suggesting that both growth factors could induce very similar if not identical signaling events.

Mixed quantum-classical study of energy transfer between H2O and a dipeptide

A mixed quantum-classical (MQC) approach is developed to study energy transfer between H2O and Gly-Ala dipeptide. In this approach, the translational motion of H2O is treated classically while the rotational motion of water and the internal torsion of the dipeptide are treated quantum mechanically. This treatment results in a mixed four-dimensional quantum and three-dimensional classical treatment. By employing the AMBER force field, the MQC approach is carried out to study rotational excitation of water and torsional excitation of the dipeptide in collision between H2O and the dipeptide. For excitation of Cα–C and Cα–N torsions, the collisions are direct. In excitation of side chain torsion, the complex collision occurs with the water being trapped near the Gla-Ala. In both direct and resonant collisions, the rotational motion of water is found to be strongly excited. This MQC approach can be extended to study collision energy transfer between rigid small molecules and peptides/protein, polymer or surface. Such theoretical studies should be very useful in understanding detailed energy transfer mechanism involving biological molecules.

Statistical analysis of the protein environment of N-glycosylation sites: implications for occupancy, structure, and folding.

We recently reported statistical analysis of structural data on glycosidic linkages. Here we extend this analysis to the glycan-protein linkage, and the peptide primary, secondary, and tertiary structures around N-glycosylation sites. We surveyed 506 glycoproteins in the Protein Data Bank crystallographic database, giving 2592 glycosylation sequons (1683 occupied) and generated a database of 626 nonredundant sequons with 386 occupied. Deviations in the expected amino acid composition were seen around occupied asparagines, particularly an increased occurrence of aromatic residues before the asparagine and threonine at position +2. Glycosylation alters the asparagine side chain torsion angle distribution and reduces its flexibility. There is an elevated probability of finding glycosylation sites in which secondary structure changes. An 11-class taxonomy was developed to describe protein surface geometry around glycosylation sites. Thirty-three percent of the occupied sites are on exposed convex surfaces, 10% in deep recesses and 20% on the edge of grooves with the glycan filling the cleft. A surprisingly large number of glycosylated asparagine residues have a low accessibility. The incidence of aromatic amino acids brought into close contact with the glycan by the folding process is higher than their normal levels on the surface or in the protein core. These data have significant implications for control of sequon occupancy and evolutionary selection of glycosylation sites and are discussed in relation to mechanisms of protein fold stabilization and regional quality control of protein folding. Hydrophobic protein-glycan interactions and the low accessibility of glycosylation sites in folded proteins are common features and may be critical in mediating these functions.

Regiochemically Well-Defined Fluorenone−Alkylthiophene Copolymers: Synthesis, Spectroscopic Characterization, and Their Postfunctionalization with Oligoaniline

A new solution processable, regioregular, alternate copolymer of fluorenone and dialkylbithiophene, namely poly[(5,5‘-(3,3‘-di-n-octyl-2,2‘-bithiophene))-alt-(2,7-fluoren-9-one)] (abbreviated as PDOBTF), was synthesized by three different preparation methods: chemical or electrochemical oxidation of 2,7-bis(4-octylthien-2-yl)-fluoren-9-one or polycondensation of 2,7-bis(5-bromo-4-octylthien-2-yl)-fluoren-9-one in the presence of Ni(0) reagent. Independent of the preparation method, the crude product is a mixture of high molecular weight fractions and short oligomers. It can be however easily fractionated into fractions differing in their molecular weight by sequential extractions with a series of solvents. The principal absorption band registered for the undoped polymer (λmax = 384 nm for the THF solution and 389 nm for the solid state) originates from the π−π* transition of the conjugated backbone and is blue-shifted because of the chain torsion effects caused by steric hindrance. This band is accompanied by a peak of smaller intensity (λmax = 476 nm for the THF solution and 485 nm for the solid state) attributed to the n−π* transition in the carbonyl group of the fluoren-9-one subunit. Preliminary photoluminescence studies show that PDOBTF exhibits a very large Stokes shift and emits red light (λmax = 631 nm in THF solution and 643 nm in the solid state). Upon chemical p-type doping with FeCl4-, the polymer reaches the conductivity of σdc = 0.05 S cm-1. Mössbauer spectroscopy studies of the doping process show that both structural subunits, i.e., the bithiophene subunit and the fluoren-9-one one, participate in the doping. PDOBTF can be relatively easily postfunctionalized by grafting aniline oligomers as pendant groups via the carbonyl groups of the fluoren-9-one subunit. By consequence, the spectrum of the modified polymer can be precisely tuned in the visible region by changing the grafting level.

Crystal Structure of Form I of Syndiotactic 1,2-Poly(4-methyl-1,3-pentadiene)

The crystal structure of the form I of syndiotactic 1,2-poly(4-methyl-1,3-pentadiene) has been determined studying the X-ray fiber diffraction pattern recorded onto a Fuji image plate. The chain conformation (T6G2T2G2), previously proposed by Meille et al. on the basis of the identity period, has been confirmed, but with deviations of chain torsion angles from the 60 and 180° values. The crystal system is triclinic, a = 17.513(8) Å, b = 9.117(6) Å, c = 11.251(14) Å, α = 95.20(4)°, β = 98.01(3)°, γ = 92.74(5)°, and V = 1768(3) Å3. The space group is P1̄, with two chains per cell, each formed by six nonequivalent CH2CH[CHC(CH3)2] chemical units. The crystal structure was determined and refined by the least-squares method, keeping bond lengths fixed and assuming that chemically equivalent bond angles are equal to each other. The refined model shows unrealistic values for some side group bond angles, in particular for the angle between methyl groups. Quite satisfactory results are obtained fixing this angle to the value of 122.7°, as suggested by searching the Cambridge Structural Database. Final disagreement indices are R1 = 14.3% and R2 = 15.0%.

Ramachandran plot on the web

A graphics package has been developed to display the main chain torsion angles phi, psi (phi, Psi); (Ramachandran angles) in a protein of known structure. In addition, the package calculates the Ramachandran angles at the central residue in the stretch of three amino acids having specified the flanking residue types. The package displays the Ramachandran angles along with a detailed analysis output. This software is incorporated with all the protein structures available in the Protein Databank.