Mirror image forms of snow flea antifreeze protein prepared by total chemical synthesis have identical antifreeze activities

The recently discovered glycine-rich snow flea antifreeze protein (sfAFP) has no sequence homology with any known proteins. No experimental structure has been reported for this interesting protein molecule. Here we report the total chemical synthesis of the mirror image forms of sfAFP (i.e., L-sfAFP, the native protein, and D-sfAFP, the native protein's enantiomer). The predicted 81 amino acid residue polypeptide chain of sfAFP contains Cys residues at positions 1, 13, 28, and 43 and was prepared from four synthetic peptide segments by sequential native chemical ligation. After purification, the full-length synthetic polypeptide was folded at 4 degrees C to form the sfAFP protein containing two disulfides. Chemically synthesized sfAFP had the expected antifreeze activity in an ice recrystallization inhibition assay. Mirror image D-sfAFP protein was prepared by the same synthetic strategy, using peptide segments made from d-amino acids, and had an identical but opposite-sign CD spectrum. As expected, D-sfAFP displays the same antifreeze properties as L-sfAFP, because ice presents an achiral surface for sfAFP binding. Facile synthetic access to sfAFP will enable determination of its molecular structure and systematic elucidation of the molecular basis of the antifreeze properties of this unique protein.     

Elucidation of the Covalent and Tertiary Structures of Biologically Active Ts3 Toxin

Ts3 is an alpha scorpion toxin from the venom of the Brazilian scorpion Tityus serrulatus. Ts3 binds to the domain IV voltage sensor of voltage‐gated sodium channels (Na_v) and slows down their fast inactivation. The covalent structure of the Ts3 toxin is uncertain, and the structure of the folded protein molecule is unknown. Herein, we report the total chemical synthesis of four candidate Ts3 toxin protein molecules and the results of structure–activity studies that enabled us to establish the covalent structure of biologically active Ts3 toxin. We also report the synthesis of the mirror image form of the Ts3 protein molecule, and the use of racemic protein crystallography to determine the folded (tertiary) structure of biologically active Ts3 toxin by X‐ray diffraction.     

(Quasi‐)Racemic X‐ray Structures of Glycosylated and Non‐Glycosylated Forms of the Chemokine Ser‐CCL1 Prepared by Total Chemical Synthesis

Our goal was to obtain the X‐ray crystal structure of the glycosylated chemokine Ser‐CCL1. Glycoproteins can be hard to crystallize because of the heterogeneity of the oligosaccharide (glycan) moiety. We used glycosylated Ser‐CCL1 that had been prepared by total chemical synthesis as a homogeneous compound containing an N‐linked asialo biantennary nonasaccharide glycan moiety of defined covalent structure. Facile crystal formation occurred from a quasi‐racemic mixture consisting of glycosylated L ‐protein and non‐glycosylated‐D ‐protein, while no crystals were obtained from the glycosylated L ‐protein alone. The structure was solved at a resolution of 2.6–2.1 Å. However, the glycan moiety was disordered: only the N‐linked GlcNAc sugar was well‐defined in the electron density map. A racemic mixture of the protein enantiomers L ‐Ser‐CCL1 and D ‐Ser‐CCL1 was also crystallized, and the structure of the true racemate was solved at a resolution of 2.7–2.15 Å. Superimposition of the structures of the protein moieties of L ‐Ser‐CCL1 and glycosylated‐L ‐Ser‐CCL1 revealed there was no significant alteration of the protein structure by N‐glycosylation.     

Quasiracemic crystallization as a tool to assess the accommodation of noncanonical residues in nativelike protein conformations

Quasiracemic crystallization has been used to obtain high-resolution structures of two variants of the villin headpiece subdomain (VHP) that contain a pentafluorophenylalanine (F(5)Phe) residue in the hydrophobic core. In each case, the crystal contained the variant constructed from l-amino acids and the native sequence constructed from d-amino acids. We were motivated to undertake these studies by reports that racemic proteins crystallize more readily than homochiral forms and the prospect that quasiracemic crystallization would enable us to determine whether a polypeptide containing a noncanonical residue can closely mimic the tertiary structure of the native sequence. The results suggest that quasiracemic crystallization may prove to be generally useful for assessing mimicry of naturally evolved protein folding patterns by polypeptides that contain unnatural side-chain or backbone subunits.     

Chemical synthesis and structural analysis of guanylate cyclase C agonist linaclotide

Linaclotide and its D-enantiomer were obtained through Fmoc solid phase peptide synthesis method and co-crystalized through racemic crystallization. The crystal structure showed that linaclotide has a tight, three-beta turns structure immobilized by three pairs of disulfide bonds.     

Synthesis of l‐ and d‐Ubiquitin by One‐Pot Ligation and Metal‐Free Desulfurization

Native chemical ligation combined with desulfurization has become a powerful strategy for the chemical synthesis of proteins. Here we describe the use of a new thiol additive, methyl thioglycolate, to accomplish one‐pot native chemical ligation and metal‐free desulfurization for chemical protein synthesis. This one‐pot strategy was used to prepare ubiquitin from two or three peptide segments. Circular dichroism spectroscopy and racemic protein X‐ray crystallography confirmed the correct folding of ubiquitin. Our results demonstrate that proteins synthesized chemically by streamlined 9‐fluorenylmethoxycarbonyl (Fmoc) solid‐phase peptide synthesis coupled with a one‐pot ligation–desulfurization strategy can supply useful molecules with sufficient purity for crystallographic studies.     

Straightforward synthesis of (R)-(-)-kjellmanianone

A direct route to enantiomerically pure (-)-kjellmanianone is reported. The synthesis involves a cerium-catalyzed alpha-hydroxylation and an enzyme-catalyzed procedure to resolve tertiary alcohols at key stages. The intermediate beta-oxo ester was alpha-hydroxylated to give good yields of racemic kjellmanianone. The resolution of the racemic material was achieved by enzymatic saponification, followed by a chemical decarboxylation sequence to give enantiopure (-)-kjellmanianone with 99 % ee. Bromination then afforded the (-)-bromo derivative, whose X-ray structure provided evidence for the R configuration of (-)-kjellmanianone.     

Effect of the air-water interface on the structure of lysozyme in the presence of guanidinium chloride

We report observations of the changes in the surface structure of lysozyme adsorbed at the air-water interface produced by the chemical denaturant guanidinium chloride. A primary result is the durability of the adsorbed surface layer to denaturation, as compared to the molecule in the bulk solution. Data on the surface film were obtained from X-ray and neutron reflectivity measurements and modeled simultaneously. The behavior of lysozyme in G.HCl solutions was determined by small-angle X-ray scattering. For the air-water interface, determination of the adsorbed protein layer dimensions shows that at low to moderate denaturant concentrations (up to 2 mol L(-1)), there is no significant distortion of the protein's tertiary structure at the interface, as changes in the orientation of the protein are sufficient to model data. At higher denaturant concentrations, time-dependent multilayer formation occurred, indicating molecular aggregation at the surface. Methodologies to predict the protein orientation at the interface, based on amino acid residues' surface affinities and charge, were critiqued and validated against our experimental data.     

A comparative investigation of Co2+ and Mn2+ incorporation into aluminophosphates by in situ XAS and DFT computation

The incorporation processes of Mn2+ and Co2+ into the framework of aluminophosphate molecular sieve AlPO4-5, at the onset of crystallization, were investigated by in situ synchrotron X-ray absorption spectroscopy (XAS) and density functional theory (DFT) computation. The results indicated that the syntheses of MnAPO-5 and CoAPO-5 were different in the incorporation mechanism of metal ions. For the synthesis of CoAPO-5, Co2+ transferred from an octahedral into tetrahedral structure with crystal formation, while, for MnAPO-5, the Mn2+ transition to the tetrahedral structure was much more difficult and it occurred after the appearance of long-range ordered microporous structure. The DFT computations of model intermediates involved in the synthesis process suggested that much higher transformation energy of [Mn(OP(OH)3)4]2+ than that of [Co(OP(OH)3)4]2+ was responsible for the diversity of the incorporation behaviors.     

Enantiomeric purity determination by NMR: proving the purity of a single enantiomer

The NMR spectra of separate samples of an analyte complexed with each enantiomer of a chiral solvating agent (CSA) give an accurate estimate of the chemical shifts of racemic analytes in the presence of a single enantiomer of the CSA. This effect allows a CSA-based chiral NMR method to be developed when only a single enantiomer of analyte is available. The ability to develop a method capable of discriminating between enantiomers in these circumstances is useful, for example, to resolve the question of whether racemization has occurred during the synthesis of a chiral molecule.     

Toward ab initio refinement of protein X-ray crystal structures: interpreting and correlating structural fluctuations

The refinement of protein crystal structures currently involves the use of empirical restraints and force fields that are known to work well in many situations but nevertheless yield structural models with some features that are inconsistent with detailed chemical analysis and therefore warrant further improvement. Ab initio electronic structure computational methods have now advanced to the point at which they can deliver reliable results for macromolecules in realistic times using linear-scaling algorithms. The replacement of empirical force fields with ab initio methods in a final refinement stage could allow new structural features to be identified in complex structures, reduce errors and remove computational bias from structural models. In contrast to empirical approaches, ab initio refinements can only be performed on models that obey basic qualitative chemical rules, imposing constraints on the parameter space of existing refinements, and this in turn inhibits the inclusion of unlikely structural features. Here, we focus on methods for determining an appropriate ensemble of initial structural models for an ab initio X-ray refinement, modeling as an example the high-resolution single-crystal X-ray diffraction data reported for the structure of lysozyme (PDB entry “2VB1”). The AMBER force field is used in a Monte Carlo calculation to determine an ensemble of 8 structures that together embody all of the partial atomic occupancies noted in the original refinement, correlating these variations into a set of feasible chemical structures while simultaneously retaining consistency with the X-ray diffraction data. Subsequent analysis of these results strongly suggests that the occupancies in the empirically refined model are inconsistent with protein energetic considerations, thus depicting the 2VB1 structure as a deep-lying minimum in its optimized parameter space that actually embodies chemically unreasonable features. Indeed, density-functional theory calculations for one specific nitrate ion with an occupancy of 62% indicate that water replaces this ion 38% of the time, a result confirmed by subsequent crystallographic analysis. It is foreseeable that any subsequent ab initio refinement of the whole structure would need to locate a globally improved structure involving significant changes to 2VB1 which correct these identified local structural inconsistencies.     

Quantum chemistry can locally improve protein crystal structures

We have re-refined the X-ray structure of the heme site in cytochrome c553, supplementing the crystallographic data with quantum chemical geometry optimizations, instead of the molecular mechanics force field used in standard crystallographic refinement. By comparing the resulting structure, obtained using medium-resolution data (170 pm), with an atomic-resolution structure (95 pm) of the same protein, we show that the inclusion of quantum chemical information into the refinement procedure improves the structure significantly. Thus, errors in the Fe-ligand distances are reduced from 3 to 32 pm in the low-resolution structure to 0-5 pm in the re-refined structure, one side-chain atom changes its conformation (a movement by 214 pm toward its position in the high-resolution structure), and the R factors are improved by up to 0.018. Thus, quantum refinement may be a powerful method to obtain an accurate structure for interesting parts of a protein.     

Chiral symmetry breaking and polymorphism in 1,1'-binaphthyl melt crystallization

We have studied chiral symmetry breaking in the melt crystallization of 1,1'-binaphthyl. We confirm that chiral symmetry breaking can be induced by stirring the melt as it crystallizes. We find an additional process of vapor crystallization to occur alongside the melt crystallization. This complicates the analysis of the enantiomorphism by introducing a further phenomenon: that of polymorphism. Crystallographic studies by X-ray diffraction reveal two polymorphs of 1,1'-binaphthyl that are made up of two different conformers of each of the two enantiomeric forms of the molecule. Crystals from the melt are generally chiral tetragonal crystals (P42(1)2(1)) composed of (R)- or (S)-1,1'-binaphthyl in a transoid conformer, while those from the vapor are racemic monoclinic crystals (C2/c) made up of the cisoid conformer of both (R)- and (S)-1,1'-binaphthyl enantiomers. The main intermolecular interactions in all these crystals are weak aromatic CH/pi hydrogen bonds, which are responsible for the enantiomeric discrimination in the molecular recognition during crystallization. A tendency for whisker crystal formation is notable in 1,1'-binaphthyl. In stirred crystallization, fluid and mechanical forces can break off these whiskers, which provide secondary nuclei for further crystallization. This autocatalytic mechanism induces chiral symmetry breaking during the crystallization.     

A chemical model for redox regulation of protein tyrosine phosphatase 1B (PTP1B) activity

Growing evidence indicates that endogenously produced hydrogen peroxide acts as a cellular signaling molecule that (among other things) can regulate the activity of some protein phosphatases. Recent X-ray crystallographic studies revealed an unexpected chemical transformation underlying the redox regulation of protein tyrosine phosphatase 1B, in which oxidative inactivation of the enzyme yields an intrastrand protein cross-link between the catalytic cysteine residue and its neighboring amide nitrogen. This work describes a small organic molecule that serves as an effective model for the redox-sensing assembly of functional groups at the active site of PTP1B. Findings obtained using this model system suggest that the oxidative transformation of PTP1B to its "crosslinked" inactive form can proceed directly via oxidation of the active-site cysteine to a sulfenic acid (RSOH). The remarkably facile nature of this protein cross-link-forming reaction, along with the widespread cellular occurrence of protein sulfenic acids generated via oxidation of cysteine residues, suggests that the type of oxidative protein cross-link formation first seen in the context of PTP1B represents a potentially general mechanism for redox "switching" of protein function. Thus, the chemistry characterized here could have broad relevance to both redox-regulated signal transduction and the toxic effects of oxidative stress.     

The separation of racemic crystals into enantiomers by chiral block copolymers

A series of chiral double hydrophilic block copolymers (DHBCs) was synthesized and employed as additives in the crystallization of calcium tartrate tetrahydrate (CaT). We found that appropriate polymers can slow down the formation of the thermodynamically most stable racemic crystals as well as the formation of one of the pure enantiomeric crystals so that chiral separation by crystallization occurs even when racemic crystals can be formed. In addition, the presence of DHBCs results in major modifications of crystal morphology, creating unusual morphologies of higher complexity. Our study demonstrates the potential application of chiral DHBCs in the control of chirality throughout crystallization, in particular for racemic crystal systems, and also shows that enantiomeric excess of one enantiomer can be maximized by the kinetic control of crystallization.     

气相转移法与水热合成法合成ZSM-5/SAPO-5核壳结构复合分子筛的比较

以磷酸、拟薄水铝石和硅溶胶为原料,三乙胺为模板剂,在不同晶化温度和晶化时间的实验条件下,分别采用水热合成法和气相转移法合成了一系列ZSM-5/SAPO-5核壳结构复合分子筛,并用X射线衍射、扫描电镜、X射线能量散射谱、红外光谱和N2吸附等手段对其进行了表征.结果表明,所合成的分子筛是以ZSM-5为核,以SAPO-5为壳的双结构复合分子筛.晶化温度的提高和晶化时间的延长有利于分子筛结晶度的提高.与水热合成法相比,采用气相转移法可以减小壳层SAPO-5的颗粒尺寸,减少脱离ZSM-5表面独立生长的SAPO-5的量,改善SAPO-5在ZSM-5表面的分布.重油裂化结果表明,核壳结构复合分子筛对生成低碳烯烃的催化性能优于机械混合的样品.     

Determination of fluid--solid transitions in model protein solutions using the histogram reweighting method and expanded ensemble simulations

Protein crystallization conditions are usually identified by empirical screening methods because of the complexity of the process, such as the existence of nonequilibrium phases and the different crystal forms that may result from changes in solution conditions. Here the crystallization of a model protein is studied using computer simulation. The model consists of spheres that have both an isotropic interaction of short range and anisotropic interactions between patch-antipatch pairs. The free energy of a protein crystal is calculated using expanded ensemble simulations of the Einstein crystal, and NpT-Monte Carlo simulations with histogram reweighting are used to determine the fluid-solid coexistence. The histogram reweighting method is also used to trace out the complete coexistence curve, including multiple crystal phases, with varying reduced temperature, which corresponds to changing solution conditions. At a patch-antipatch interaction strength five times that of the isotropic interaction, the protein molecules form a stable simple cubic structure near room temperature, whereas an orientationally disordered face-centered-cubic structure is favored at higher temperatures. The anisotropic attractions also lead to a weak first-order transition between orientationally disordered and ordered face-centered-cubic structures at low temperature, although this transition is metastable. A complete phase diagram, including a fluid phase, three solid phases, and two triple points, is found for the six-patch protein model. A 12-patch protein model, consistent with the face-centered-cubic structure, leads to greater thermodynamic stability of the ordered phase. Metastable liquid-liquid phase equilibria for isotropic models with varying attraction tails are also predicted from Gibbs ensemble simulations.     

Crystal and molecular structure of N-(benzylimidazolyl-2)-O-methylcarbamate salts

Single crystal X-ray diffraction has been applied to determine the structure of salts — formate and hydrochloride of N-(benzylimidazolyl-2)-O-methylcarbamate (BMC). The crystal structure of BMC formate is built by a molecule of a base and two formic acid molecules, one of them protonating a BMC molecule. Hydrogen bonds in the crystal form a weakly bound one-dimensional ribbon. BMC hydrochloride crystallizes as dihydrate. Two molecules of crystallization water and Cl ion make a robust H-bonded two-dimensional layer. BMC salts are formed through the protonation of N9 atom.     

Racemic DNA Crystallography

Racemates increase the chances of crystallization by allowing molecular contacts to be formed in a greater number of ways. With the advent of protein synthesis, the production of protein racemates and racemic‐protein crystallography are now possible. Curiously, racemic DNA crystallography had not been investigated despite the commercial availability of L ‐ and D ‐deoxyribo‐oligonucleotides. Here, we report a study into racemic DNA crystallography showing the strong propensity of racemic DNA mixtures to form racemic crystals. We describe racemic crystal structures of various DNA sequences and folded conformations, including duplexes, quadruplexes, and a four‐way junction, showing that the advantages of racemic crystallography should extend to DNA.     

Racemic DNA Crystallography

Racemates increase the chances of crystallization by allowing molecular contacts to be formed in a greater number of ways. With the advent of protein synthesis, the production of protein racemates and racemic‐protein crystallography are now possible. Curiously, racemic DNA crystallography had not been investigated despite the commercial availability of L ‐ and D ‐deoxyribo‐oligonucleotides. Here, we report a study into racemic DNA crystallography showing the strong propensity of racemic DNA mixtures to form racemic crystals. We describe racemic crystal structures of various DNA sequences and folded conformations, including duplexes, quadruplexes, and a four‐way junction, showing that the advantages of racemic crystallography should extend to DNA.