Enhanced Hydrolytic Stability of Short‐Chain Poly[(R)‐3‐hydroxybutyrate] Conjugated to Native E. coli Cytoplasmic Proteins

Many prokaryotic and eukaryotic proteins are modified by post‐translational conjugation to short‐chain poly[(R)‐3‐hydroxybutyrate] (cPHB). The relative lability of ester bonds raises the concern that the cPHB may be substantially degraded by chemical hydrolysis during protein purification, thus increasing the difficulty of its detection and measurement. Here, we compare rates of acid‐ and base‐catalyzed hydrolysis of cPHB conjugated to native and denatured proteins at room temperature. E. coli cytoplasmic proteins, native or denatured by addition of guanidium hydrochloride, were treated with aqueous solutions of H₂SO₄ or NaOH at concentrations ranging from 0.1–2.0n . The loss of cPHB was measured as a function of time by a chemical assay. We find that cPHB conjugated to native proteins is surprisingly resistant to both acid‐ and base‐catalyzed hydrolysis, whereas cPHB conjugated to denatured proteins is proficiently degraded at rates proportional to acid or base concentration. The results suggest that cPHB occupies a highly protective environment within native proteins.     

溶液中变性剂浓度对蛋白溶菌酶复性的影响

Based on three-state renaturation process of denatured proteins, an equation describing the effect of denaturant concentration on renaturation yield of denatured proteins was presented. By this equation, two parameters n（m1 -m2） and Ka can be obtained. The former indicates the difference in the number of denaturant molecules between the renaturation process of n number of refolding intermediates from refolding intermediate state to native state and their aggregate process from refolding intermediate state to aggregate state, the latter denotes the apparent aggregate equilibrium constant for protein molecules aggregated from native state to aggregate state, and from them, the characteristics of the renaturation process of denatured proteins in denaturant solution can be identified. This equation was tested by the renaturation processes of denatured egg white lysozyme in guanidine hydrochloride and urea solutions, with the results to show that when guanidine hydrochloride and urea concentrations were separately higher than 1.25 and 3.00 mol/L or separately lower than 1.00 and 3.00 mol/L, the refolding intermediates of egg white lysozymes were more easily aggregated to aggregate state or more easily renatured to native state, respectively. Under different initial total egg white lysozyme concentrations in urea solution, the refolding egg white lysozyme intermediates could be deduced to have a tendency to form a bimolecular intermediate aggregate, and this inference was further confirmed by their nonreducing SDS-PAGE and size exclusion chromatography.     

Molecular Simulations and Drug Discovery of Adenosine Receptors

G protein-coupled receptors (GPCRs) represent the largest family of human membrane proteins. Four subtypes of adenosine receptors (ARs), the A₁AR, A_2AAR, A_2BAR and A₃AR, each with a unique pharmacological profile and distribution within the tissues in the human body, mediate many physiological functions and serve as critical drug targets for treating numerous human diseases including cancer, neuropathic pain, cardiac ischemia, stroke and diabetes. The A₁AR and A₃AR preferentially couple to the G_i/o proteins, while the A_2AAR and A_2BAR prefer coupling to the G_s proteins. Adenosine receptors were the first subclass of GPCRs that had experimental structures determined in complex with distinct G proteins. Here, we will review recent studies in molecular simulations and computer-aided drug discovery of the adenosine receptors and also highlight their future research opportunities.     

Interaction identification of Zif268 and TATAZF proteins with GC‐/AT‐rich DNA sequence: A theoretical study

Molecular dynamics (MD) simulations for Zif268 (a zinc‐finger‐protein binding specifically to the GC‐rich DNA)‐d(A₁G₂C₃G₄T₅G₆G₇G₈C₉A₁₀C₁₁)₂ and TATA_ZF (a zinc‐finger‐protein recognizing the AT‐rich DNA)‐d(A₁C₂G₃C₄T₅A₆T₇A₈A₉A₁₀A₁₁G₁₂G₁₃)₂ complexes have been performed for investigating the DNA binding affinities and specific recognitions of zinc fingers to GC‐rich and AT‐rich DNA sequences. The binding free energies for the two systems have been further analyzed by using the molecular mechanics Poisson‐Boltzmann surface area (MM‐PBSA) method. The calculations of the binding free energies reveal that the affinity energy of Zif268‐DNA complex is larger than that of TATA_ZF‐DNA one. The affinity between the zinc‐finger‐protein and DNA is mainly driven by more favorable van‐der‐Waals and nonpolar/solvation interactions in both complexes. However, the affinity energy difference of the two binding systems is mainly caused by the difference of van‐der‐Waals interactions and entropy components. The decomposition analysis of MM‐PBSA free energies on each residue of the proteins predicts that the interactions between the residues with the positive charges and DNA favor the binding process; while the interactions between the residues with the negative charges and DNA behave in the opposite way. The interhydrogen‐bonds at the protein‐DNA interface and the induced intrafinger hydrogen bonds between the residues of protein for the Zif268‐DNA complex have been identified at some key contact sites. However, only the interhydrogen‐bonds between the residues of protein and DNA for TATA_ZF‐DNA complex have been found. The interactions of hydrogen‐bonds, electrostatistics and van‐der‐Waals type at some new contact sites have been identified. Moreover, the recognition characteristics of the two studied zinc‐finger‐proteins have also been discussed. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

Single‐Molecule Detection Reveals Knot Sliding in TrmD Denaturation

An increasing number of proteins are found to contain a knot in their polypeptide chain. Although some studies have looked into the folding mechanism of knotted proteins, why and how these complex topologies form are still far from being fully answered. Moreover, no experimental information about how the knot moves during the protein‐folding process is available. Herein, by combining single‐molecule fluorescence resonance energy transfer (smFRET) experiments with molecular dynamics (MD) simulations, we performed a detailed study to characterize the knot in the denatured state of TrmD, a knotted tRNA (guanosine‐1) methyltransferase from Escherichia coli, as a model system. We found that the knot still existed in the unfolded state of TrmD, consistent with the results for two other knotted proteins, YibK and YbeA. More interestingly, both smFRET experiments and MD simulations revealed that the knot slid towards the C‐terminal during the unfolding process, which could be explained by the relatively strong interactions between the β‐sheet core at the N terminal of the native knot region. The size of the knot in the unfolded state is not larger than that in the native state. In addition, the knot slid in a “downhill” mode with simultaneous chain collapse in the denatured state.     

Semisynthesis of Functional Glycosylphosphatidylinositol‐Anchored Proteins

Glypiation is a common posttranslational modification of eukaryotic proteins involving the attachment of a glycosylphosphatidylinositol (GPI) glycolipid. GPIs contain a conserved phosphoglycan that is modified in a cell‐ and tissue‐specific manner. GPI complexity suggests roles in biological processes and effects on the attached protein, but the difficulties to get homogeneous material have hindered studies. We disclose a one‐pot intein‐mediated ligation (OPL) to obtain GPI‐anchored proteins. The strategy enables the glypiation of folded and denatured proteins with a natural linkage to the glycolipid. Using the strategy, glypiated eGFP, Thy1, and the Plasmodium berghei protein MSP1₁₉ were prepared. Glypiation did not alter the structure of eGFP and MSP1₁₉ proteins in solution, but it induced a strong pro‐inflammatory response in vitro. The strategy provides access to glypiated proteins to elucidate the activity of this modification and for use as vaccine candidates against parasitic infections.     

Molecular Structure of Amyloid Fibrils Formed by Residues 127 to 147 of the Human Prion Protein

Amyloid fibrils are filamentous and insoluble forms of peptides or proteins. Proline has long been considered to be incompatible with the cross‐β structural motif of amyloid fibrils. On the basis of solid‐state NMR spectroscopy data, we present a structural model of an in‐register parallel β sheet for the amyloid fibrils formed from a human prion protein fragment, huPrP_127–47. We have developed a simple solid‐state NMR spectroscopy technique to identify solvent‐protected backbone amide protons in a H/D exchange experiment without disaggregating the amyloid fibrils, from which we find that proline residue P₁₃₇ does not disrupt the β‐sheet structure from G₁₂₇ to G₁₄₂. We suggest that the resultant kink at P₁₃₇ generates a twist between adjacent peptide strands to maintain hydrogen bonding in the β‐sheet regions flanking the P₁₃₇ residue. Although proline can be well integrated into the cross‐β structure of amyloid fibrils, the kink formed at the position of the proline residue will considerably weaken the hydrogen bonding between the neighboring strands, especially when the mutation site is near the central region of a β sheet.     

Pulsed hydrogen/deuterium exchange mass spectrometry for time‐resolved membrane protein folding studies

Kinetic folding experiments by pulsed hydrogen/deuterium exchange (HDX) mass spectrometry (MS) are a well‐established tool for water‐soluble proteins. To the best of our knowledge, the current study is the first that applies this approach to an integral membrane protein. The native state of bacteriorhodopsin (BR) comprises seven transmembrane helices and a covalently bound retinal cofactor. BR exposure to sodium dodecyl sulfate (SDS) induces partial unfolding and retinal loss. We employ a custom‐built three‐stage mixing device for pulsed‐HDX/MS investigations of BR refolding. The reaction is triggered by mixing SDS‐denatured protein with bicelles. After a variable folding time (10 ms to 24 h), the protein is exposed to excess D₂O buffer under rapid exchange conditions. The HDX pulse is terminated by acid quenching after 24 ms. Subsequent off‐line analysis is performed by size exclusion chromatography and electrospray MS. These measurements yield the number of protected backbone N–H sites as a function of folding time, reflecting the recovery of secondary structure. Our results indicate that much of the BR secondary structure is formed quite late during the reaction, on a time scale of 10 s and beyond. It is hoped that in the future it will be possible to extend the pulsed‐HDX/MS approach employed here to membrane proteins other than BR. Copyright © 2012 John Wiley & Sons, Ltd.     

Reactivity of Singlet Oxygen Toward Proteins: The Effect of Structure in Basic Pancreatic Trypsin Inhibitor and in Ribonuclease A

The reactions of singlet oxygen, ¹O₂, with large peptides have been described previously. It was found that even in these systems, which in their native form are generally not supposed to possess a stable structure in solution, the polypeptide does impede the access of ¹O₂ to the amino acids that react readily with ¹O₂. Here we describe the ¹0₂ reaction with two proteins of well-defined structure. The quenching of ¹O₂ by bovine pancreatic trypsin inhibitor (BPTI) and by ribonuclease A (RNase A) was compared to that of a solution at the same concentration as those of its constituent amino acids that react readily with ¹O₂. The proteins were studied in their native form, when partly denatured by splitting their S-S bonds and when fully denatured. It was found that while in the native form the quenching rate constant was seven times lower in BPTI (2.2 vs 15.2 times 10⁷WM^-1 s^-1) and three times lower in RNase A (11.0 vs 32 times 10⁷M^-l s^-1) than in a mixture of its constituent amino acid residues, it increased upon denaturation reaching in the fully denatured state the value of the corresponding amino acid mixture. More striking is the effect of the protein structure when comparing the fraction of the encounters between ¹O₂ and protein, which cause damage to the protein, as reflected in the decrease of its biological activity. This decrease is assumed to be due to the chemical (oxidative) reactions of ¹O₂ in the protein. In the exceptionally stable BPTI the fraction of such encounters was 0.05 and in RNase A it was 0.2, whereas for the amino acid tryptophan in solution, 0.7 of the collisions with ¹O₂ led to a chemical reaction.     

On molecular topological properties of hex‐derived networks

Topological indices are numerical parameters of a molecular graph, which characterize its topology and are usually graph invariant. In quantitative structure–activity relationship/quantitative structure–property relationship study, physico‐chemical properties and topological indices such as Randić, atom–bond connectivity (ABC), and geometric–arithmetic (GA) index are used to predict the bioactivity of chemical compounds. Graph theory has found a considerable use in this area of research. In this paper, we study hex‐derived networks HDN1(n) and HDN2(n), which are generated by hexagonal network of dimension n and derive analytical closed results of general Randić index R_α(G) for different values of α, for these networks of dimension n. We also compute the general first Zagreb, ABC, GA, ABC₄, and GA₅ indices for these hex‐derived networks for the first time and give closed formulae of these degree‐based indices for hex‐derived networks. Copyright © 2016 John Wiley & Sons, Ltd.     

Multicanonical parallel simulations of proteins with continuous potentials

The determination of the three‐dimensional (3D) structure of a protein or peptide is a very important research problem in biological and medical sciences. Anfinsen's experiments (Science 1973, 181, 223) on renaturation of denatured proteins have shown that the native 3D structure of a (small) protein at low (room) temperatures is uniquely determined by its amino acid sequence, which suggests that it might be possible to determine the 3D structure of a protein from its amino acid sequence by pure computations. As a step toward that goal, in this article we present a simple approach for parallelization of multicanonical Monte Carlo simulations of proteins with continuous potentials. Our method is based on the parallel calculation of the protein energy function. The algorithm is tested by simulated annealing and multicanonical simulations of two small peptides, and known results are reproduced accurately. An acceptable degree of parallelization can be achieved in the simulation of Protein L using up to 30 PCs. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1287–1296, 2001     

Dual Binding Mode of Metallacarborane Produces a Robust Shield on Proteins

An inorganic sandwich molecule, Na[Co(C₂B₉H₁₁)₂], able to produce vesicles through self-assembly and known to produce strong dihydrogen-bond interactions with amine groups is capable of interacting with proteins. This dual non-bonding ability of Na[Co(C₂B₉H₁₁)₂] is what makes this molecule unique: it can be firmly anchored to a protein surface and is capable of extending over it. To prove this, the widely available bovine serum albumin (BSA), which has many pendant amino groups in its structure, has been taken as the model protein. It has been found that around 100 molecules of Na[Co(C₂B₉H₁₁)₂] preserve the native structure of BSA, while endorsing it with a significantly increased stability with respect to chemical- and thermal-induced denaturation due to efficient encapsulation. The advantages of this encapsulation technique are two-fold; the first is its simplicity as it relies on the anchoring capacity of Na[Co(C₂B₉H₁₁)₂] to the surface of the protein through the amine-containing residues and the second is its self-assembling capacity allowing it to spread across the surface. The dense shield of protection offered by Na[Co(C₂B₉H₁₁)₂] has been demonstrated by the inhibition of BSA pseudo-esterase activity, which indicates that the inorganic corset around BSA protects its reactive surface residues, thereby preventing their acetylation.     

An unconventional ligand-binding mechanism of substrate-binding proteins: MD simulation and Markov state model analysis of BtuF

In conventional “Venus Flytrap” mechanism, substrate-binding proteins (SBPs) interconvert between the open and closed conformations. Upon ligand binding, SBPs form a tightly closed conformation with the ligand bound at the interface of two domains. This mechanism was later challenged by many type III SBPs, such as the vitamin B₁₂-binding protein BtuF, in which the apo- and holo-state proteins adopt very similar conformations. Here, we combined molecular dynamics simulation and Markov state model analysis to study the conformational dynamics of apo- and B₁₂-bound BtuF. The results indicate that the crystal structures represent the only stable conformation of BtuF. Meanwhile, both apo- and holo-BtuF undergo large-scale interdomain motions with little energy cost. B₁₂ binding casts little restraints on the interdomain motions, suggesting that ligand binding affinity is enhanced by the remaining conformational entropy of holo-BtuF. These results reveal a new paradigm of ligand recognition mechanism of SBPs. © 2019 Wiley Periodicals, Inc.     

Refolding of detergent‐denatured lysozyme using β‐cyclodextrin‐assisted ion exchange chromatography

Chromatography‐based protein refolding is widely used. Detergent is increasingly used for protein solubilization from inclusion bodies. Therefore, it is necessary to develop a refolding method for detergent‐denatured/solubilized proteins based on liquid chromatography. In the present work, sarkosyl‐denatured/dithiothreitol‐reduced lysozyme was used as a model, and a refolding method based on ion exchange chromatography, assisted by β‐cyclodextrin, was developed for refolding detergent‐denatured proteins. Many factors affecting the refolding, such as concentration of urea, concentration of β‐cyclodextrin, pH and flow rate of mobile phases, were investigated to optimize the refolding conditions for sarkosyl‐denatured lysozymes. The results showed that the sarkosyl‐denatured lysozyme could be successfully refolded using β‐cyclodextrin‐assisted ion exchange chromatography. Copyright © 2012 John Wiley & Sons, Ltd.     

Preparation and properties of novel thermotropic liquid crystalline hyperbranched polyesters composed of five‐membered heterocyclic mesogen by A2 + B3 approach

New thermotropic liquid crystalline (LC) hyperbranched (HB) polyesters containing 2,5‐diphenyl‐1,3,4‐thiadiazole (DTD) unit as mesogen in the interiors were prepared at various mole ratios (A₂/B₃) by melt and solution polycondensations of a dioxydiundecanol of DTD (A₂) and 1,2,3‐propanetricarboxylic acid (B₃) via the A₂ + B₃ approach and their LC and optical properties were investigated. FTIR and ¹H‐NMR spectroscopies indicated that all the expected HB polyesters, which show good solubilities in organic solvents, are produced without gelation during the polymerization. Among them, the HB polymer prepared in the mole ratio of A₂/B₃ = 3/2 by the solution polycondensation had the highest inherent viscositiy. DSC measurents, polarizing microscope observations of optical textures, and X‐ray analyses suggested that the LC properties of HB polymers depend on the polymerization methods and the feed mole ratios. In the HB polymers prepared using the melt polycondensation, only the polymer prepared in the mole ratio of A₂/B₃ = 3/1 formed a highly‐ordered, tilted, crystal‐like smectic phase, but all the polymers prepared by the solution polycondensation formed highly‐ordered, tilted, smectic phases. Solution and solid‐state UV‐vis and photoluminescent (PL) spectra indicated that the HB polymers show maximum absorbances and blue‐light emission on the basis of the DTD unit, where the Stokes‐shifts were observed, probably because of intermolecular aggregation effects © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 2998–3008, 2007     

Extending the Pressure–Temperature State Diagram of Myoglobin

The pressure–temperature (P,T) diagram of proteins proposed by Hawley concerns the equilibrium between native and denatured forms. However, the importance of protein aggregation is increasingly recognized, and it has been suggested that certain aggregated states represent alternative folds of the polypeptide chain. Here, we present a P,T‐diagram for myoglobin in which we include the aggregated state and suggest to call it a P,T‐state diagram, as not all boundaries are true equilibrium transitions. We observe by Fourier transform infrared spectroscopy that increasing temperature causes the protein to aggregate, but that a subsequent further temperature increase results in the dissociation of this aggregate. Moreover, we observe that moderate pressures stabilize myoglobin against thermal denaturation. We hypothesize that this effect originates from the volume changes associated with the aggregation transition.     

Undecahalo‐closo‐undecaborates [B11Hal11]2–

The closo‐undecaborate A₂[B₁₁H₁₁] (A = NBzlEt₃) can be halogenated with excess N‐chlorosuccine imide, bromine or iodine, respectively, to give the perhalo‐closo‐undecaborates A₂[B₁₁Hal₁₁] (Hal = Cl, Br, I). The chlorination in the 11 : 1 ratio of the reagents yields A₂[B₁₁HCl₁₀], whose subsequent iodination makes A₂[B₁₁Cl₁₀I] available. The three type [B₁₁Hal₁₁]^2– anions show only one and the two type [B₁₁Cl₁₀X]^2– anions (X = H, I) only two ¹¹B NMR peaks in the ratio 10 : 1, thus exhibiting the same degenerate rearrangement of the octadecahedral B₁₁ skeleton as is well‐known for [B₁₁H₁₁]^2–. The crystal structure analysis of A₂[B₁₁Br₁₁] and A₂[B₁₁I₁₁] reveals a rigid octadecahedral skeleton in the solid state, up to 330 K, whose B–B bond lengths deviate more or less from the idealized C_2v gas phase structure, but are in good accordance with the distances of A₂[B₁₁H₁₁]. Electrochemical experiments elucidate the mechanism of the known oxidation of [B₁₁H₁₁]^2– to give [B₂₂H₂₂]^2–: A first one‐electron transfer is followed by the dimerization of the [B₁₁H₁₁]^– monoanion, whereas neutral B₁₁H₁₁, a presumably most reactive species, does not play a role as an intermediate. The electrochemical oxidation of [B₁₁Hal₁₁]^2– anions also starts with a one‐electron transfer, which is perfectly reversible only in the case of Hal = Br. There is no electrochemical indication for the formation of [B₂₂Hal₂₂]^2–. The neutral species B₁₁Hal₁₁ should be a short‐lived, very reactive species.     

Accessible Mannitol‐Based Amphiphiles (MNAs) for Membrane Protein Solubilisation and Stabilisation

Integral membrane proteins are amphipathic molecules crucial for all cellular life. The structural study of these macromolecules starts with protein extraction from the native membranes, followed by purification and crystallisation. Detergents are essential tools for these processes, but detergent‐solubilised membrane proteins often denature and aggregate, resulting in loss of both structure and function. In this study, a novel class of agents, designated mannitol‐based amphiphiles (MNAs), were prepared and characterised for their ability to solubilise and stabilise membrane proteins. Some of MNAs conferred enhanced stability to four membrane proteins including a G protein‐coupled receptor (GPCR), the β₂ adrenergic receptor (β₂AR), compared to both n‐dodecyl‐d ‐maltoside (DDM) and the other MNAs. These agents were also better than DDM for electron microscopy analysis of the β₂AR. The ease of preparation together with the enhanced membrane protein stabilisation efficacy demonstrates the value of these agents for future membrane protein research.     

Conformation and Topology of Diacylglycerol Kinase in E.coli Membranes Revealed by Solid‐state NMR Spectroscopy

Solid‐state NMR is a powerful tool for studying membrane proteins in a native‐like lipid environment. 3D magic angle spinning (MAS) NMR was employed to characterize the structure of E.coli diacylglycerol kinase (DAGK) reconstituted into its native E.coli lipid membranes. The secondary structure and topology of DAGK revealed by solid‐state NMR are different from those determined by solution‐state NMR and X‐ray crystallography. This study provides a good example for demonstrating the influence of membrane environments on the structure of membrane proteins.