Crystal structure studies of amino acids and peptides

Modeling and Analysis of HIV-1 Pol Polyprotein as a Case Study for Predicting Large Polyprotein Structures

Acquired immunodeficiency syndrome (AIDS) is caused by human immunodeficiency virus (HIV). HIV protease, reverse transcriptase, and integrase are targets of current drugs to treat the disease. However, anti-viral drug-resistant strains have emerged quickly due to the high mutation rate of the virus, leading to the demand for the development of new drugs. One attractive target is Gag-Pol polyprotein, which plays a key role in the life cycle of HIV. Recently, we found that a combination of M50I and V151I mutations in HIV-1 integrase can suppress virus release and inhibit the initiation of Gag-Pol autoprocessing and maturation without interfering with the dimerization of Gag-Pol. Additional mutations in integrase or RNase H domain in reverse transcriptase can compensate for the defect. However, the molecular mechanism is unknown. There is no tertiary structure of the full-length HIV-1 Pol protein available for further study. Therefore, we developed a workflow to predict the tertiary structure of HIV-1 NL4.3 Pol polyprotein. The modeled structure has comparable quality compared with the recently published partial HIV-1 Pol structure (PDB ID: 7SJX). Our HIV-1 NL4.3 Pol dimer model is the first full-length Pol tertiary structure. It can provide a structural platform for studying the autoprocessing mechanism of HIV-1 Pol and for developing new potent drugs. Moreover, the workflow can be used to predict other large protein structures that cannot be resolved via conventional experimental methods.

High-resolution structure of the amino acid transporter AdiC reveals insights into the role of water molecules and networks in oligomerization and substrate binding

Background

The L-arginine/agmatine transporter AdiC is part of the arginine-dependent extreme acid resistance system of the bacterium Escherichia coli and its pathogenic varieties such as strain E. coli O157:H7. At the present time, there is a lack of knowledge concerning the role of water molecules and networks for the structure and function of AdiC, and solute transporters in general.

Results

The structure of the L-arginine/agmatine transporter AdiC was determined at 1.7 Å resolution by X-ray crystallography. This high resolution allowed for the identification of numerous water molecules buried in the structure. In combination with molecular dynamics (MD) simulations, we demonstrate that water molecules play an important role for stabilizing the protein and key residues, and act as placeholders for atoms of the AdiC substrates L-arginine and agmatine. MD simulations unveiled flexibility and restrained mobility of gating residues W202 and W293, respectively. Furthermore, a water-filled cavity was identified at the dimer interface of AdiC. The two monomers formed bridging interactions through water-mediated hydrogen bonds. The accessibility and presence of water molecules in this cavity was confirmed with MD simulations. Point mutations disrupting the interfacial water network validated the importance of water molecules for dimer stabilization.

Conclusions

This work gives new insights into the role and importance of water molecules in the L-arginine/agmatine transporter AdiC for protein stabilization and substrate-binding site shaping and as placeholders of substrate atoms. Furthermore, and based on the observed flexibility and restrained mobility of gating residues, a mechanistic role of the gate flexibility in the transport cycle was proposed. Finally, we identified a water-filled cavity at the dimeric interface that contributes to the stability of the amino acid transporter oligomer.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-021-01102-4.

Supramolecular organization of α-galactosylceramide in pure dispersions and in cationic DODAB bilayers

α-galactosylceramide (α-GalCer; KRN7000) strongly stimulates NKT cells. The structures of α-GalCer assemblies and of cationic DODAB bilayers containing α-GalCer were investigated by differential scanning calorimetry (DSC) and electron spin resonance (ESR) spectroscopy. Assemblies of α-GalCer have a very tightly packed gel phase, causing spin labels to cluster and display spin exchange interactions. An endothermic phase transition is observed by DSC, leading to a fluid phase. This phase transition peak disappears upon mixing with DODAB, showing that up to 9 mol% α-GalCer is miscible with the cationic lipid. ESR spectra show that α-GalCer decreases DODAB gel phase packing, resulting in a decrease of gel-fluid transition temperature and cooperativity in DSC thermograms of mixed bilayers. In contrast, α-GalCer increases the rigidity of the fluid phase. These effects are probably due to the conformation of the rigid amide bond that connects the phytosphingosine base of α-GalCer to its long and saturated acyl chain. Possibly, α-GalCer adopts a V-shaped conformation because of the perpendicular orientation of the amide bond towards the axes of the hydrocarbon chains. Apparently, the effect of the amide bond configuration is a key structural feature for the interaction between ceramide-based glycolipids and DODAB molecules, since we have previously reported a similar decrease of gel phase packing and increase in fluid phase rigidity for DODAB bilayers containing C24:1β-glucosylceramide. Since the structure of delivery systems is critical to the biological activity of α-GalCer, this work certainly contributes to the planning and development of novel immunotherapeutic tools.

Affinity of Smectite and Divalent Metal Ions (Mg(2+), Ca(2+), Cu(2+)) with L-leucine: An Experimental and Theoretical Approach Relevant to Astrobiology

Earth is the only known planet bestowed with life. Several attempts have been made to explore the pathways of the origin of life on planet Earth. The search for the chemistry which gave rise to life has given answers related to the formation of biomonomers, and their adsorption on solid surfaces has gained much attention for the catalysis and stabilization processes related to the abiotic chemical evolution of the complex molecules of life. In this communication, surface interactions of L-leucine (Leu) on smectite (SMT) group of clay (viz. bentonite and montmorillonite) and their divalent metal ion (Mg(2+), Ca(2+) and Cu(2+)) incorporated on SMT has been studied to find the optimal conditions of time, pH, and concentration at ambient temperature (298 K). The progress of adsorption was followed spectrophotometrically and further characterized by FTIR, SEM/EDS and XRD. Leu, a neutral/non polar amino acid, was found to have more affinity in its zwitterionic form towards Cu(2+)- exchanged SMT and minimal affinity for Mg(2+)- exchanged SMT. The vibrational frequency shifts of -NH3 (+) and -COO(-) favor Van der Waal's forces during the course of surface interaction. Quantum calculations using density functional theory (DFT) have been applied to investigate the absolute value of metal ion affinities of Leu (Leu-M(2+) complex, M = Mg(2+), Ca(2+), Cu(2+)) with the help of their physico-chemical parameters. The hydration effect on the relative stability and geometry of the individual species of Leu-M(2+) × (H2O)n, (n =2 and 4) has also been evaluated within the supermolecule approach. Evidence gathered from investigations of surface interactions, divalent metal ions affinities and hydration effects with biomolecules may be important for better understanding of chemical evolution, the stabilization of biomolecules on solid surfaces and biomolecular-metal interactions. These results may have implications for understanding the origin of life and the preservation of biomarkers.

Quantum mechanics of excitation transport in photosynthetic complexes: a key issues review

For a long time microscopic physical descriptions of biological processes have been based on quantum mechanical concepts and tools, and routinely employed by chemical physicists and quantum chemists. However, the last ten years have witnessed new developments on these studies from a different perspective, rooted in the framework of quantum information theory. The process that more, than others, has been subject of intense research is the transfer of excitation energy in photosynthetic light-harvesting complexes, a consequence of the unexpected experimental discovery of oscillating signals in such highly noisy systems. The fundamental interdisciplinary nature of this research makes it extremely fascinating, but can also constitute an obstacle to its advance. Here in this review our objective is to provide an essential summary of the progress made in the theoretical description of excitation energy dynamics in photosynthetic systems from a quantum mechanical perspective, with the goal of unifying the language employed by the different communities. This is initially realized through a stepwise presentation of the fundamental building blocks used to model excitation transfer, including protein dynamics and the theory of open quantum system. Afterwards, we shall review how these models have evolved as a consequence of experimental discoveries; this will lead us to present the numerical techniques that have been introduced to quantitatively describe photo-absorbed energy dynamics. Finally, we shall discuss which mechanisms have been proposed to explain the unusual coherent nature of excitation transport and what insights have been gathered so far on the potential functional role of such quantum features.

Peroxoniobium(v)-catalyzed selective oxidation of sulfides with hydrogen peroxide in water: a sustainable approach

Facile and selective transformation of thioethers to the corresponding sulfoxides or sulfones with 30% H₂O₂ has been achieved in an aqueous medium by using peroxoniobium(v) complexes as reusable catalysts.

Peptide formation mechanism on montmorillonite under thermal conditions

The oligomerization of amino acids is an essential process in the chemical evolution of proteins, which are precursors to life on Earth. Although some researchers have observed peptide formation on clay mineral surfaces, the mechanism of peptide bond formation on the clay mineral surface has not been clarified. In this study, the thermal behavior of glycine (Gly) adsorbed on montmorillonite was observed during heating experiments conducted at 150 °C for 336 h under dry, wet, and dry-wet conditions to clarify the mechanism. Approximately 13.9 % of the Gly monomers became peptides on montmorillonite under dry conditions, with diketopiperazine (cyclic dimer) being the main product. On the other hand, peptides were not synthesized in the absence of montmorillonite. Results of IR analysis showed that the Gly monomer was mainly adsorbed via hydrogen bonding between the positively charged amino groups and negatively charged surface sites (i.e., Lewis base sites) on the montmorillonite surface, indicating that the Lewis base site acts as a catalyst for peptide formation. In contrast, peptides were not detected on montmorillonite heated under wet conditions, since excess water shifted the equilibrium towards hydrolysis of the peptides. The presence of water is likely to control thermodynamic peptide production, and clay minerals, especially those with electrophilic defect sites, seem to act as a kinetic catalyst for the peptide formation reaction.

Crystal structure analyses of some addition compounds of glycine

The crystal structure of three addition compounds of glycine, viz., bisglycine barium(II) dichloride monohydrate, (NH3 +CH2COO−)2Ba++Cl2 − · H2O; bisglycine strontium(II) dichloride trihydrate, (NH3 +CH2COO−)2Sr++Cl2 − · 3H2O;and bisglycine manganese(II) dichloride, (NH3+CH2COO−)2Mn++Cl2 −, hereafter refered as GlycBa, GtycSr and GlycMn, respectively, were solved by single-crystal x-ray diffraction methods and refined to R values of 0.034, 0.058 and 0.074, respectively, using visually estimated and counter measured intensity data. GlycBa and GlycSr crystallize in the orthorhombic system of space group Pbcn, with four formula units per unit cell of dimensions a = 8.31, b = 14.84 and c = 9.32 Å; and a = 16.42, b = 9.35 and c = 8.26 Å, respectively, and GlycMn crystallizes in the triclinic system of space group P[unk], with one formula unit per unit cell of dimensions a = 4.97, b = 7.92 and c = 6.98 Å, α = 107.4, β = 115.9 and γ = 87.0°. The glycine molecule is almost planar except for the nitrogen atom, which deviates by 0.145, 0.113 and 0.677 Å. The conformation of the glycine molecule is synplanar with conformation angle of 5.8, 6.7 and 29.2° and the molecule exists in zwitterion configuration in these structures. Nitrogen, chlorine and water-oxygen atoms take part in the hydrogen-bond formation and only one of the carboxyl-oxygen atoms is acceptor of an hydrogen bond in GlycBa and GlycSr whereas both the carboxyl-oxygen atoms are acceptors of hydrogen bonds in GlycMn. The average values of N…O, N…Cl, OCl and O…O bonds are 2.86, 3.21, 3.23 and 2.84 Å, respectively.

The coordination number is 9 in GlycBa and GlycSr and is 6 in GlycMn. Oxygen and chlorine atoms are coordinated to the metal ion in GlycBa and GlycMn and chlorine atoms do not enter into coordination with the metal ion in GlycSr. The coordination polyhedron around Ba ion can be visualized as a distorted antiprism with an extra atom and around Sr ion as a distorted antiprism with an extra atom or as a distorted regular prism and around Mn ion as an octahedron. Glycine residue acts as a bidentate, forming four-membered chelate rings with metal ions in GlycBa and GlycSr and acts as an unidentate in GlycMn.

Conformational flexibility of Y145Stop human prion protein amyloid fibrils probed by solid-state nuclear magnetic resonance spectroscopy

Amyloid aggregates of a C-truncated Y145Stop mutant of human prion protein, huPrP23-144, associated with a heritable amyloid angiopathy, have previously been shown to contain a compact, relatively rigid, and beta-sheet-rich approximately 30-residue amyloid core near the C-terminus under physiologically relevant conditions. In contrast, the remaining huPrP23-144 residues display considerable conformational dynamics, as evidenced by the absence of corresponding signals in cross-polarization (CP)-based solid-state NMR (SSNMR) spectra under ambient conditions and their emergence in analogous spectra recorded at low temperature on frozen fibril samples. Here, we present the direct observation of residues comprising the flexible N-terminal domain of huPrP23-144 amyloid by using 2D J-coupling-based magic-angle spinning (MAS) SSNMR techniques. Chemical shifts for these residues indicate that the N-terminal domain is effectively an ensemble of protein chains with random-coil-like conformations. Interestingly, a detailed analysis of signal intensities in CP-based 3D SSNMR spectra suggests that non-negligible molecular motions may also be occurring on the NMR time scale within the relatively rigid core of huPrP23-144 amyloid. To further investigate this hypothesis, quantitative measurements of backbone dipolar order parameters and transverse spin relaxation rates were performed for the core residues. The observed order parameters indicate that, on the submicrosecond time scale, these residues are effectively rigid and experience only highly restricted and relatively uniform motions similar to those characteristic for well-structured regions of microcrystalline proteins. On the other hand, significant variations in magnitude of transverse spin relaxation rates were noted for residues present at different locations within the core region and correlated with observed differences in spectral intensities. While interpreted only qualitatively at the present time, the extent of the observed variations in transverse relaxation rates is consistent with the presence of relatively slow, microsecond-millisecond time scale chemical exchange type phenomena within the huPrP23-144 amyloid core.

Direct separation of captopril diastereoisomers including their rotational isomers by RP-LC using a teicoplanin column

A direct reversed-phase liquid chromatography (LC) method has been developed for the separation and analysis of captopril and its 2R,2S diastereoisomer using a teicoplanin stationary phase. The proline containing diastereoisomers, which are known to form conformers in aqueous solution, were also separated from their rotational isomers. The influence of temperature, different organic modifiers and buffer type, concentration and pH were optimised to obtain a working resolution between the two diastereoisomers and their respective rotational isomers. The diastereoisomeric purity of several commercial captopril batches was subsequently evaluated using a 0.05% triethylammonium acetate (TEAA) buffer (pH 3.8) run at 1.0 ml/min with mobile phase reservoir and column temperature controlled at 0 degrees C. Throughout the study online UV diode array and mass spectrometry detection was carried out simultaneously to confirm that peaks eluting from the teicoplanin column were in fact captopril and not its readily converted disulphide dimer. Additionally, as a result of the greater detection sensitivity of mass spectrometry, it also facilitated a more accurate optimisation study where trace amounts of the rotational isomers were found to be present in the baseline at temperatures higher than optimum.

Reengineering a type II beta-turn as a potential helix nucleator. Part I. Crystal structure of Boc-Val-Pro-(D)Asp-Asp-Val-OMe monohydrate

The crystal structure of Boc-Val1-Pro2-(D)Asp3-Asp4-Val5-OMe is described as a type II beta-turn reengineered into a potential helix nucleator. (D)Asp3 in the peptide is responsible for the configurationally guided LD chiral type II beta-turn centered at Pro2-(D)Asp3, as well as the partially developed LL chiral type I beta-turn centered at Asp4-Val5 by acceptance of a conformation nucleating H-bond from Val5NH to its carboxylic oxygen.

Conformation and hydrogen bonding of N-formylpeptides: crystal and molecular structure of N-formyl-L-alanyl-L-aspartic acid

Crystals of N-formyl-L-alanyl-L-aspartic acid (C8H11N2O6) grown from aqueous methanol solution are orthorhombic, space group, P2(1)2(1)2(1) with cell parameters at 294K of a = 13.619(2), b = 8.567(2), c = 9.583(3)A, V = 1118.1A3, M.W. = 232.2, Z = 4, Dm = 1.38 g/cm3 and Dx = 1.378 g/cm3. The crystal structure was solved by the application of direct methods and refined to an R value of 0.075 for 1244 reflections with I greater than or equal to 3 sigma collected on a CAD-4 diffractometer. The structure contains two short intermolecular hydrogen bonds: (i) between the C-terminal carboxyl OH and the N-acyl oxygen (2.624(3)A), a characteristic feature found in many N-acyl peptides and (ii) between the aspartic carboxyl OH. and the peptide oxygen OP1 (2.623(3)A). The peptide is nonplanar (omega = 165.5(6) degrees). The molecule takes up a folded conformation in contrast to N-formyl peptides which form extended beta-sheets; the values of phi 1, psi 1, phi 2, psi 2(1), and psi 2(2) are, respectively -65.7(6), 152.0(5), -107.2(5), 30.9(5), and -150.3(6). The aspartic acid side chain conformation is g- with chi 1 = 73.1(5). The formyl group, as expected, is transplanar [OF-CF-N1-CA1 = -4.0(8) degrees]. The presence of the short O-H ... O hydrogen bond emerges as a structural feature common to this peptide and several other N-formyl peptides. There are no C-H ... O hydrogen bonds in this structure.

17O- and 14N-NMR studies of Leu-enkephalin and enkephalin-related fragments in aqueous solution

17O- and 14N-nmr chemical shifts and line widths of the carboxyl and amino terminal groups of Leu-enkephalin--Tyr-Gly-Gly-Phe-[17O]Leu-Oh--and enkephalin-related fragments--[17O]Leu-OH, Phe-[17O]Leu-OH, Gly-Phe-[17O]Leu-OH, and Gly-Gly-Phe-[17O]Leu-OH--were measured in aqueous solution over the entire H pH range. Enrichment in 17O was achieved by saponification of the corresponding O-methyl esters. Ionization constants and titration shifts were obtained by nonlinear least-squares fits to one-proton titration curves. [17O]Leu-OH exhibits a profound pH-dependent solvation change on deprotonation of the carboxyl group, as shown by 17O- and 14N-nmr line widths. In contrast, the peptides studied do not exhibit pH-dependent conformational (solvation) changes on deprotonation of the carboxyl group, and a head-to-tail intramolecular association between the ionic terminal groups should be excluded. It is shown that the peptides do not exhibit isotropic overall molecular motion and that segmental motion rather than fast internal motion influences the effective correlation times at the sites of the carboxyl oxygens and the amino nitrogen.