Jumping between protein conformers using normal modes

The relationship between the normal modes of a protein and its functional conformational change has been studied for decades. However, using this relationship in a predictive context remains a challenge. In this work, we demonstrate that, starting from a given protein conformer, it is possible to generate in a single step model conformers that are less than 1 Å (C_α ‐RMSD) from the conformer which is the known endpoint of the conformational change, particularly when the conformational change is collective in nature. Such accurate model conformers can be generated by following either the so‐called robust or the 50 lowest‐frequency modes obtained with various Elastic Network Models (ENMs). Interestingly, the quality of many of these models compares well with actual crystal structures, as assessed by the ROSETTA scoring function and PROCHECK. The most accurate and best quality conformers obtained in the present study were generated by using the 50 lowest‐frequency modes of an all‐atom ENM. However, with less than ten robust modes, which are identified without any prior knowledge of the nature of the conformational change, nearly 90% of the motion described by the 50 lowest‐frequency modes of a protein can be captured. Such results strongly suggest that exploring the robust modes of ENMs may prove efficient for sampling the functionally relevant conformational repertoire of many proteins. © 2017 Wiley Periodicals, Inc.     

Two‐Dimensional Crowding Uncovers a Hidden Conformation of α‐Synuclein

The intrinsically disordered protein (IDP), α‐synuclein (αS), is well‐known for phospholipid membrane binding‐coupled folding into tunable helical conformers. Here, using single‐molecule experiments in conjunction with ensemble assays and a theoretical model, we present a unique case demonstrating that the interaction–folding landscape of αS can be tuned by two‐dimensional (2D) crowding through simultaneous binding of a second protein on the bilayer surface. Unexpectedly, the experimental data show a clear deviation from a simple competitive inhibition model, but are consistent with a bimodal inhibition mechanism wherein membrane binding of a second protein (a membrane interacting chaperone, Hsp27, in this case) differentially inhibits two distinct modules of αS–membrane interaction. As a consequence, αS molecules are forced to access a hidden conformational state on the phospholipid bilayer in which only the higher‐affinity module remains membrane‐bound. Our results demonstrate that macromolecular crowding in two dimensions can play a significant role in shaping the conformational landscape of membrane‐binding IDPs with multiple binding modes.     

枯草杆菌α-淀粉酶在一些色谱体系中的热力学和超热力学研究

通过测定不同温度范围的热力学平衡常数、焓变、熵变、自由能变和补偿温度,研究了枯草杆菌α-淀粉酶在几种色谱介质上的热力学和超热力学。结果表明,在RP-C18反相介质、Zn2+螯合的Sepharose fast-flow亲和介质和WCX-1阳离子交换介质上,当温度分别在13-30和30-50℃范围时,它们的lnKSL分别随绝对温度的倒数线性变化;而在PEG-400和修饰的PEG-400疏水色谱介质上,当温度分别在13-40和13-30℃范围时,它们的lnKSL分别随绝对温度的倒数线性减小,但当温度分别高于40℃和30℃时,它们则随绝对温度的倒数剧烈减小。通过研究不同温度范围的焓变、熵变、自由能变和α-淀粉酶构象变化之间的关系,发现在RP-C18反相和Zn2+螯合的Sepharose fast-flow亲和介质上在30- 50 ℃温度范围内,在WCX-1阳离子交换介质上在13-30 ℃温度范围内,α-淀粉酶的吸附过程由焓变和熵变共同所支配,而在Zn2+螯合的Sepharose fast-flow亲和介质上在13- 30 ℃温度范围内,在WCX-1阳离子交换介质上在30-50 ℃温度范围和在PEG-400 和修饰的PEG-400疏水色谱介质上在13-65 ℃温度范围时,α-淀粉酶的吸附过程仅仅由熵变所控制。最后,通过α-淀粉酶在这些色谱体系中的补偿温度进一步发现,它们的焓变仅仅只能通过它们构象变化所引起的熵变所补偿。     

A non‐planar peptide bond in l‐seryl‐l‐valine

The C^α—C′—N—C^α (ω) torsion angle of the peptide bond in the crystal structure of the title compound, C₈H₁₆N₂O₄, is 157.37 (15)°. This is the second‐largest deviation from planarity observed for a small linear peptide.     

Studies on the Thermodenaturation Behavior of Bacillus subtilis α‐Amylase on Chromatographic Media

The thermodenaturation behavior of Bacillus subtilis α‐amylase on some chromatographic media was studied by determining their adsorption parameters with frontal analysis. The experimental results show that on a RP‐C₁₈ reversed‐phase medium, a Chelating Sepharose Fast‐Flow chelated by Zn²⁺ affinity medium and a WCX‐1 cation‐exchange medium, a stable conformation of α‐amylase molecule separately exists below or over 30 °C; while on a PEG‐400 hydrophobic medium and a modified PEG‐400 medium, a stable conformation of α‐amylase molecule separately exists below 40 and 30 °C, and when the experimental temperatures are separately over 40 and 30 °C, a drastically conformational change of α‐amylase molecules can continuously take place. And by combining the intrinsic fluorescence emission spectrum and thermal inactivation profile of α‐amylase in free solution and on the PEG‐400 and modified PEG‐400 hydrophobic media, it can be concluded that in liquid chromatographic procedure, chromatographic media can induce the conformational change of α‐amylase molecules and promote their thermodenaturation; and in hydrophobic interaction chromatography, the higher the hydrophobicity of chromatographic medium, the lower the conformational change temperature of α‐amylase molecules on the chromatographic medium.     

Multiisotopic modeling of fragmentation ion patterns in mass spectra of organometallic and coordination compounds

Investigation of hardly interpretable complex patterns can lead to an explanation of details of fragmentation and, therefore, the identification of ion clusters can be a significant procedure of mass spectra interpretation. The modeling presented remains a simple tool for mass spectra interpretation and determination of parameters of complex cluster components. Good adjustment of model to experimental data suggests that such components must be considered in the pattern interpretation; approach results in the model fits within a 1% precision for the cluster of two or more components. Applications of the Multiisotopic Modeling of Fragmentation Ion Patterns (MMFIP method) are presented for bis(dibutyldithiophosphate)‐zinc(II)‐[(C₄H₉O)₂PS₂]₂Zn, 1′,1‴‐dibenzylbiferrocene‐C₃₄H₃₀Fe₂ and 1,1′,2,2′,3,3′‐hexachloroferrocene‐C₁₀H₄Cl₆Fe as examples. It seems that the isotopic cluster modeling based on the least squares method can be a helpful aid for determination of the complex pattern components. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 354–365, 2001     

The isomeric compounds nimbolide and isonimbolide

Nimbolide [systematic name: (4α,5α,6α,7α,15β,17α)‐7,15:21,23‐diepoxy‐6‐hydroxy‐4,8‐dimethyl‐1‐oxo‐18,24‐dinor‐11,12‐secochola‐2,13,20,22‐tetraene‐4,11‐dicarboxylic acid γ‐lactone methyl ester], C₂₇H₃₀O₇, was isolated from the leaves of Azadirachta indica, and its isomer, isonimbolide [systematic name: (4α,5α,6α,7α,15α)‐7,15:21,23‐diepoxy‐6‐hydroxy‐4,8‐dimethyl‐1‐oxo‐18,24‐dinor‐11,12‐secochola‐2,16,20,22‐tetra­ene‐4,11‐dicarboxylic acid γ‐lactone methyl ester], was prepared from a novel rearrangement reaction of nimbolide, using boron trifluoride etherate and tetra­butyl­ammonium bromide. The reaction conditions are probably responsible for the ether cleavage, double‐bond rearrangement and reformation of the ether linkage. As a result, there are conformational changes in two cyclo­pentane rings and the side‐chain –CH₂COOMe group. In isonimbolide, an (24) hydrogen‐bond motif is observed.     

Electron predators are hydrogen atom traps. Effects of aryl groups on N—Cα bond dissociations of peptide radicals

Effects of substituted aryl groups on dissociations of peptide aminoketyl radicals were studied computationally for model tetrapeptide intermediates GXD^?G where X was a cysteine residue that was derivatized by S‐(3‐nitrobenzyl), S‐(3‐cyanobenzyl), S‐(3,5‐dicyanobenzyl), S‐(2,3,4,5,6‐pentafluorobenzyl), and S‐benzyl groups. The aminoketyl radical was placed within the Asp amide group. Aminoketyl radicals having the S‐(3‐nitrobenzyl) group were found to undergo spontaneous and highly exothermic migration of the hydroxyl hydrogen atom onto the nitro group in conformers allowing interaction between these groups. Competing reaction channels were investigated for aminoketyl radicals having the S‐(3‐cyanobenzyl) and S‐(3,5‐dicyanobenzyl) groups, e.g. H‐atom migration to the C and N atoms of the C≡N group, migration to the C‐4 position of the phenyl ring, and dissociation of the radical‐activated N? C_α bond between the Asp and Gly residues. RRKM kinetic analysis on the combined B3LYP and ROMP2/6‐311++G(2d,p) potential energy surface indicated > 99% H‐atom transfer to the C≡N group forming a stable iminyl intermediate. The N? C_α bond dissociation was negligible. In contrast, peptides with the S‐(2,3,4,5,6‐pentafluorobenzyl) and S‐benzyl groups showed preferential N? C_α bond dissociation that outcompeted H‐atom migration to the C‐4 position and fluorine substituents in the phenyl ring. These computational results are used to suggest an alternative mechanism for the quenching effect on electron‐based peptide backbone dissociations of benzyl groups with electron‐withdrawing substitutents, as reported recently. Copyright © 2010 John Wiley & Sons, Ltd.     

Calculations on the Nonlinear Second—Order Optical Polarizabilities for Series of Donor—C60 Molecules

IntroductionThebulkpreparation1ofC6 0 andC70 clusters(fullerenes)hasstimulatedawidevarietyofexperimentalandtheoreticalstudies .2 5Wehavesuccessfullyexaminedthestructures ,UV visiblespectraandthenonlinearthird orderopticalpolarizabilities (γ)ofC6 0 andC70 .6 ,7Byin troductionofsubstituents ,thecentrosymmetriesofC6 0 andC70 arebrokenandthesecond orderopticalnonlinearitiesareinduced .ThechargeseparationinsubstitutedC6 0whichleadstoenhancementofβvaluehasalsobeendis cussed .5Inrecentyears ,a…     

Chiral discrimination in hydrogen‐bonded complexes of 2‐methylol oxirane with hydrogen peroxide

A systematic quantum chemical study reveals the effects of chirality on the intermolecular interactions between two chiral molecules bound by hydrogen bonds. The methods used are second‐order Møller–Plesset perturbation theory (MP2) with the 6‐311++g(d,p) basis set. Complexes via the O? H···O hydrogen bond formed between the chiral 2‐methylol oxirane (S) and chiral HOOH (P and M) molecules have been investigated, which lead to four diastereomeric complexes. The nomenclature of the complexes used in this article is enantiomeric configuration sign corresponding to English letters. Such as: sm, sp. The relative positions of the methylol group and the hydrogen peroxide are designated as syn (same side) and anti (opposite side). The largest chirodiastaltic energy was ΔE_chir = ?1.329 kcal mol^?1 [9% of the counterpoise correct average binding energy D_e(corr)] between the sm‐syn and sp‐anti in favor of sm‐syn. The largest diastereofacial energy was ?1.428 kcal mol^?1 between sm‐syn and sm‐anti in favor of sm‐syn. To take into account solvents effect, the polarizable continuum model (PCM) method has been used to evaluate the chirodiastaltic energies, and diastereofacial energies of the 2‐methylol oxirane···HOOH complexes. The chiral 2,3‐dimethylol oxirane (S, S) is C₂ symmetry which offers two identical faces. Hence, the chirodiastaltic energy is identical to the diastereomeric energy, and is ΔE_chir = 0.563 kcal mol^?1 or 5.3% of the D_e(corr) in favor of s,s‐p. The optimized structures, interaction energies, and chirodiastaltic energies for various isomers were estimated. The harmonic frequencies, IR intensities, rotational constants, and dipole moments were also reported. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Simulated Raman spectra of four tetraphenylbutadiene polymorphs

We report a combined experimental and theoretical investigation on the Raman spectra of the polymorphs α, β, γ, and δ of 1,1,4,4‐tetraphenyl‐1,3‐butadiene (TPB), in the region of the intramolecular modes. The interpretation of the polarized spectra is supported by ab‐initio calculations for the isolated molecules and by lattice dynamics calculations for the crystals. The calculations reproduce the peculiar, and surprisingly large, differences among the spectra of the various polymorphs. The phenyl groups of 1,1,4,4‐tetraphenyl‐1,3‐butadiene may arrange themselves around the butadiene skeleton in 2 stable conformers, which have either inversion (C_i) or 2‐fold (C₂) symmetry and therefore exhibit intramolecular vibrations with quite different Raman selection rules and spectra. The compound forms 4 crystalline polymorphs (α, β, γ, and δ) with different combinations of C_i and C₂ conformers, and correspondingly different intramolecular spectra. The theoretical calculations provide a quantitative analysis of the various spectra.     

The first N‐terminal unprotected (Gly‐Aib)n peptide: H‐Gly‐Aib‐Gly‐Aib‐OtBu

Glycine (Gly) is incorporated in roughly half of all known peptaibiotic (nonribosomally biosynthesized antibiotic peptides of fungal origin) sequences and is the residue with the greatest conformational flexibility. The conformational space of Aib (α‐aminoisobutyric acid) is severely restricted by the second methyl group attached to the C_α atom. Most of the crystal structures containing Aib are N‐terminal protected. Deprotection of the N‐ or C‐terminus of peptides may alter the hydrogen‐bonding scheme and/or the structure and may facilitate crystallization. The structure reported here for glycyl‐α‐aminoisobutyrylglycyl‐α‐aminoisobutyric acid tert‐butyl ester, C₁₆H₃₀N₄O₅, describes the first N‐terminal‐unprotected (Gly‐Aib)_n peptide. The achiral peptide could form an intramolecular hydrogen bond between the C=O group of Gly1 and the N—H group of Aib4. This hydrogen bond is found in all tetrapeptides and N‐terminal‐protected tripeptides containing Aib, apart from one exception. In the present work, this hydrogen bond is not observed (N...O = 5.88 Å). Instead, every molecule is hydrogen bonded to six other symmetry‐related molecules with a total of eight hydrogen bonds per molecule. The backbone conformation starts in the right‐handed helical region (and the left‐handed helical region for the inverted molecule) and reverses the screw sense in the last two residues.     

Synthesis,Electronic, and Morphological Properties of Tetrahedral Oligothiophenes with n‐Hexyl Terminal Groups

A series of tetrahedral oligothiophenes bearing n‐hexyl groups at the α‐positions of the terminal thiophene rings, (n‐C₆H₁₃(C₄H₂S)_n)₄C (Hex‐TnTM; n=1–4), has been synthesized by Kosugi–Migita–Stille coupling as a key reaction. Thanks to the improved solubility afforded by the terminal n‐hexyl groups, the largest homologue (n=4) was successfully obtained. Whereas the smaller derivatives (n=1, 2) were obtained as liquid substances, the larger derivatives (n=3, 4) were obtained as solids. Hex‐T3 TM partially adopts syn conformations between the adjacent thiophene rings in the crystal, probably owing to the packing force. Hex‐T3 TM not only appeared in the crystalline state but also the amorphous state, which was stable to up to 80 °C. Regardless of the terminal groups, the derivatives of n=2 exhibited a broad fluorescence with large Stokes shifts compared to the corresponding linear analogues, thereby suggesting the presence of intramolecular interactions between the bithiophene moieties. Interactions between terthiophene branches was also suggested in the radical cations of Hex‐T3 TM by cyclic voltammetry measurements.     

A Ring‐Flippable Sugar as a Stimuli‐Responsive Component of Liposomes

For the development of a liposome that takes in and out a drug in response to stimuli, 2,4‐diaminoxylose (Xyl), which allows stimuli‐responsive conformational switches between ⁴C₁ and ¹C₄, was incorporated into a lipid structure: Xyl derivatives with C8 and C16 methylene chains at the 1,3‐positions (C8Xyl and C16Xyl) were synthesized. ¹H NMR spectroscopy indicates that the addition of Zn²⁺ and then H⁺ induces conformational switches from the chair (⁴C₁) to the reverse chair (¹C₄) and ¹C₄‐to‐⁴C₁, respectively, at Xyl; this leads to transformation of the lipids between linear and bent structures. Osmotic pressure and electron microscopy studies demonstrate that C8Xyl in water forms spherical solid aggregates (C8Xyl?Zn), which are converted into liposomes (C8Xyl+Zn) upon the addition of Zn²⁺, and C16Xyl forms liposomes regardless of the presence of Zn²⁺. The aggregates of C8Xyl±Zn incorporated a fluorophore and only C8Xyl+Zn released the content upon the addition of HCl. This study shows that Xyl could be a stimuli‐responsive component of a liposome.     

Wormlike Micelle Formation and Rheological Behavior in the Aqueous Solutions of Mixed Sulfate Gemini Surfactant without Spacer Group and Dodecyltrimethylammonium Bromide

The rheological behavior of the aqueous solutions of mixed sulfate gemini surfactant with no spacer group, referred to as d‐C₁₂S, and dodecyltrimethylammonium bromide (C₁₂TABr) at a total concentration of 100 mmol·L⁻¹ but different molar ratios of C₁₂TABr to d‐C₁₂S (α₁) was investigated using steady rate and frequency sweep measurements. The wormlike micelles were formed over a narrow α₁ range of 0.20–0.27. The viscoelastic solutions exhibited Maxwell fluid behavior. At the optimum molar ratio of 0.25, the zero‐shear viscosity was as high as 600 Pa·s and the length of the mixed wormlike micelle was about 0.45–0.85 µm. The present result provides an example to construct long wormlike micelles by anionic gemini surfactant.     

Molecular structure and barriers to internal rotation of α-naphthalenesulfonyl chloride: a study by gas-phase electron diffraction and quantum chemical calculations

α-Naphthalenesulfonyl chloride, α-NaphSC, was studied by gas-phase electron diffraction (GED) and quantum chemical calculations (HF/6-311 + G**, HF/aug-cc-pVDZ, B3LYP/cc-pVDZ, B3LYP/cc-pVTZ, B3LYP/aug-cc-pVDZ, B3LYP/aug-cc-pVTZ, MP2/cc-pVDZ, and MP2/cc-pVTZ). The calculations predict the existence of two conformers with C ₁ (I) and C _s (II) symmetries. The most stable conformer I has an enantiomer. The experimental data of α-NaphSC obtained at 370(5) K could be best fitted by a C ₁ symmetry model indicating that only this form exists in the gas-phase. In this model the C_α–S–Cl plane deviates from the perpendicular orientation relative to the plane of the naphthalene skeleton. Under the applied experimental conditions, the mole fraction of a second less stable conformer II of α-NaphSC predicted by calculations is no more than 1 %. The following geometrical parameters of conformer I were obtained from the experiment (Å and °; uncertainties are in parentheses): r _h1(C–H) = 1.082(6), r _h1(C–C)_cp = 1.407(3), r _h1(C–S) = 1.764(5), r _h1(S–O)_av = 1.425(3), r _h1(S–Cl) = 2.051(5), ∠C–C_α–C = 122.5(1), ∠C_α–S–Cl = 101.5(10); C9–C1–S–Cl = 71.4(21). The calculated barriers to internal rotation of the sulfonyl chloride group exceed considerably the thermal energy values corresponding to the temperatures of the GED experiments. Natural bond orbitals analysis of the electron density distribution was carried out to explain the peculiarities of the molecular structure of the studied compound and the deviation from the structures of β-NaphSHal molecules and their benzene analogs.     

Theoretical evidence for bond stretch isomerism in Grubbs olefin metathesis

A comprehensive density functional theory study on the dissociative and associative mechanisms of Grubbs first and second generation olefin metathesis catalysis reveals that ruthenacyclobutane intermediate (RuCB) observed in the Chauvin mechanism is not unique as it can change to a non‐metathetic ruthenacyclobutane (RuCB′) via the phenomenon of bond stretch isomerism (BSI). RuCB and RuCB′ differ mainly in RuC_α, RuC_β, and C_αC_β bond lengths of the metallacycle. RuCB is metathesis active due to the agostic type bonding‐assisted simultaneous activation of both C_αC_β bonds, giving hypercoordinate character to C_β whereas an absence of such bonding interactions in RuCB′ leads to typical CC single bond distances and metathesis inactivity. RuCB and RuCB′ are connected by a transition state showing moderate activation barrier. The new mechanistic insights invoking BSI explains the non‐preference of associative mechanism and the requirement of bulky ligands in the Grubbs catalyst design. The present study lifts the status of BSI from a concept of largely theoretical interest to a phenomenon of intense importance to describe an eminent catalytic reaction. © 2017 Wiley Periodicals, Inc.     

Conformational Relaxation of p‐Phenylenevinylene Trimers in Solution Studied by Picosecond Time‐Resolved Fluorescence

Two p‐phenylenevinylene (PV) trimers, containing 3′‐methylbutyloxyl (in MBOPV3) and 2′‐ethylhexyloxyl (in EHOPV3) side chains, are used as model compounds of PV‐based conjugated polymers (PPV) with the purpose of clarifying the origin of fast (picosecond time) components observed in the fluorescence decays of poly[2‐methoxy‐5‐(2′‐ethylhexyloxy)‐p‐phenylenevinylene] (MEH‐PPV). The fluorescence decays of MBOPV3 and EHOPV3 reveal the presence of similar fast components, which are assigned to excited‐state conformational relaxation of the initial population of non‐planar trimer conformers to lower‐energy, more planar conformers. The rate constant of conformational relaxation k_CR is dependent on solvent viscosity and temperature, according to the empirical relationship k_CR=aη_o^?α?exp(?αE_η/RT), where aη_o^?α is the frequency factor, η_o is the pre‐exponential coefficient of viscosity, E_η is the activation energy of viscous flow. The empirical parameter α, relating the solvent microscopic friction involved in the conformational change to the macroscopic solvent friction (α=1), depends on the side chain. The fast component in the fluorescence decays of MEH‐PPV polymers (PPVs), is assigned to resonance energy transfer from short to longer polymer segments. The present results call for revising this assignment/interpretation to account for the occurrence of conformational relaxation, concurrently with energy transfer, in PPVs.     

Theory of relaxation properties of two‐dimensional polymer networks, 1. Normal modes and relaxation times

The local relaxation properties of polymer networks with a two‐dimensional connectivity are considered. We use the mesh‐like network model in which the average positions of junctions form the regular spatial structure consisting of square repeating units (network cells). The two‐dimensional polymer network consisting of “bead and spring” Rouse chains and the simplified coarse‐grained network model describing only the large‐scale collective relaxation of a network are studied. For both dynamic network models the set of relaxation times and the transformation from Cartesian coordinates of network elements to normal modes are obtained. Using the normal mode transformation obtained, in Part 2 of this series the exact analytical expressions for various local dynamic characteristics of the polymer network having a two‐dimensional connectivity will be calculated.     

A conformational NMR analysis of methymycin aglycones: complete and unambiguous assignments of stereochemically diverse glycosylated methymycin analogs by 1D and 2D NMR techniques and molecular modeling

The ¹H and ¹³C NMR spectra of 10‐deoxymethynolide (1), 8.9‐dihydro‐10‐deoxymethynolide (2) and its glycosylated derivatives (3–9) were analyzed using gradient‐selected NMR techniques, including 1D TOCSY, gCOSY, 1D NOESY (DPFGSENOE), NOESY, gHMBC, gHSQC and gHSQC‐TOCSY. The NMR spectral parameters (chemical shifts and coupling constants) of 1–9 were determined by iterative analysis. For the first time, complete and unambiguous assignment of the ¹H NMR spectrum of 10‐deoxymethynolide (1) has been achieved in CDCl₃, CD₃OD and C₆D₆ solvents. The ¹H NMR spectrum of 8,9‐dihydro‐10‐deoxymethynolide (2) was recorded in CDCl₃, (CD₃)₂CO and CD₃OD solutions to determine the conformation. NMR‐based conformational analysis of 1 and 2 in conjugation with molecular modeling concluded that the 12‐membered ring of the macrolactones may predominantly exist in a single stable conformation in all solvents examined. In all cases, a change in solvent caused only small changes in chemical shifts and coupling constants, suggesting that all glycosylated methymycin analogs exist with similar conformations of the aglycone ring in solution. Copyright © 2013 John Wiley & Sons, Ltd.