Structure and properties of composites compression‐molded from silk fibroin powder and waterborne polyurethane

The degummed silk filament was pulverized with a home‐made machine to obtain the silk fibroin (SF) powder with the diameter of around 3 µm. The resulting SF powder was blended with waterborne polyurethane (WPU) aqueous dispersion, and then was dried and compression‐molded to prepare novel blended materials with improved miscibility and mechanical properties. WPU acted as a plasticizer and one of the components for the blends during the compression‐molded process. The structure, morphology, and properties of the blended films were investigated. The results indicated that β‐sheet of SF existed in the blended films. The SEM images showed that the cross‐section of the blended films exhibited an overall homogeneous morphology. Furthermore, the transmission electron microscope observation exhibited that some sphere‐like SF particles were well dispersed in the WPU matrix. The hydrogen bond interaction between SF and WPU in the blended films led to an increase of the glass transition temperature for the soft segment of WPU in the blended films. The blended films showed an improved Young's modulus and tensile strength from 1.2 to 288.9 MPa and 0.3 to 16.5 MPa, respectively, with the increasing of SF up to a content of 70 wt%. The hydrogen‐bonding interactions existing in SF and WPU and compression molding method played the important role in improving the miscibility and mechanical properties of the blended films. Copyright © 2011 John Wiley & Sons, Ltd.     

Engineering a β‐Helical d,l‐Peptide for Folding in Polar Media

β Helices—helices formed by alternating d,l ‐peptides and stabilized by β‐sheet hydrogen bonding—are found naturally in only a handful of highly hydrophobic peptides. This paper explores the scope of β‐helical structure by presenting the first design and biophysical characterization of a hydrophilic d,l ‐peptide, 1 , that forms a β helix in methanol. The design of 1 is based on the β‐hairpin/β helix—a new supersecondary that had been characterized previously only for hydrophobic peptides in nonpolar solvents. Incorporating polar residues in 1 provided solubility in methanol, in which the peptide adopts the expected β‐hairpin/β‐helical structure, as evidenced by CD, analytical ultracentrifugation (AUC), NMR spectroscopy, and NMR‐based structure calculations. Upon titration with water (at constant peptide concentration), the structure in methanol ( 1 m ) transitions cooperatively to an extended conformation ( 1 w ) resembling a cyclic β‐hairpin; observation of an isodichroic point in the solvent‐dependent CD spectra indicates that this transition is a two‐state process. In contrast, neither 1 m nor 1 w show cooperative thermal melting; instead, their structures appear intact at temperatures as high as 65 °C; this observation suggests that steric constraint is dominant in stabilizing these structures. Finally, the ¹H NMR CαH spectroscopic resonances of 1 m are downfield‐shifted with respect to random‐coil values, a hitherto unreported property for β helices that appears to be a general feature of these structures. These results show for the first time that an appropriately designed β‐helical peptide can fold stably in a polar solvent; furthermore, the structural and spectroscopic data reported should prove useful in the future design and characterization of water‐soluble β helices.     

Conformational transition of polyelectrolytes in mixed solvent by dielectric spectroscopy: Electrostatic and hydrophobic interactions

We studied conformational transition of poly(acrylic acid)‐graft‐dodecyl (PAA‐g‐dodecyl), and PAA‐graft‐poly(ethylene oxide)‐graft‐dodecyl (PAA‐g‐PEO‐g‐dodecyl) molecules in DMF/H₂O solvent by dielectric analysis method utilizing a double‐layer polarization theory. In addition to the hydrophobic interaction which has been demonstrated to be vital for their conformational transition with water content, it is confirmed that the electrostatic interaction is crucial. For PAA‐g‐dodecyl molecules, at a critical value of water content, a peak value of correlation length is reached originating from the delicate balance between electrostatic and hydrophobic interactions. For PAA‐g‐PEO‐g‐dodecyl molecules, chains conformation is mainly determined by electrostatic interaction over the entire range of water content due to the low content of dodecyl groups. Meanwhile, H‐bond associative interaction prevents the dissociation of free carboxyl groups over the range of lower water content, thus their stretched transition moves to higher water content. Our results provide the underlying insights needed to understand solvent effect on the conformational transition for polyelectrolytes with hydrophobic groups. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2019 , 57, 1716–1724     

应用光谱和分子模拟法研究一种聚酰亚胺聚合物与人免疫球蛋白的相互作用

本文利用荧光猝灭法、红外光谱法及计算机模拟技术研究了一种聚酰亚胺聚合物(2,6-Bis(4-amino-2-trifluoromethyl phenoxy-4’- benzoyl)-pyridine,简称BAFP )与人免疫球蛋白（HIgG）的相互作用。同步荧光的结果定性地说明了BAFP影响水溶液中HIgG二级结构的情况。而判定BAFP影响HIgG二级结构的定量依据来自红外光谱,实验数据表明α螺旋结构的含量相比未加入药物时增加了约2.6～10.2%,,β折叠增大了约13.6～27.7%,,而β转角则减小了约23.8～30.3%。分子模拟的结果显示BAFP与HIgG的键合作用很强,并且有四个氢键在BAFP与HIgG分子的色氨酸Trp 170, 缬氨酸Val 105, 甲硫氨酸Met 139 及天冬酰胺Asn 52之间形成;同时也显示出维持药物与蛋白质的相互作用力主要是疏水作用,这与实验所得到的热力学参数判定作用力的结果相一致（依据范德霍夫公式计算得 与 的值分别为-6.70KJ.mol-1 和 71.93 J.mol-1.K-1）。     

The Solvent‐Dependent Shift of the Amide I Band of a Fully Solvated Peptide as a Local Probe for the Solvent Composition in the Peptide/Solvent Interface

We determine the shift and line shape of the amide I band of a model AK peptide from molecular dynamics (MD) simulations of the peptide dissolved in methanol/water mixtures with varying composition. The IR spectra are determined from a transition dipole coupling exciton model. A simplified empirical model Hamiltonian is employed, which takes into account both the effect of hydrogen bonding and the intramolecular vibrational coupling. We consider a single isolated AK peptide in a mostly helical conformation, while the solvent is represented by 2600 methanol or water molecules, simulated for a pressure of 1 bar and a temperature of 300 K. Over the course of the simulations, minor reversible conformational changes at the termini are observed, which are found to only slightly affect the calculated spectral properties. Over the entire composition range, which varies from pure water to the pure methanol solvent, a monotonous shift towards higher frequency of the IR amide I band of about 8 wavenumbers is observed. This shift towards higher frequency is comparable to the shift found in preliminary experimental data also presented here on the amide I′ band. The shift is found to be caused by two counter‐compensating effects. An intramolecular red shift of about 1.2 wavenumbers occurs, due to stronger intramolecular hydrogen bonding in a methanol‐rich environment. Dominating, however, is the intermolecular solvent‐dependent shift towards higher frequency of about 10 wavenumbers, which is attributed to the less effective hydrogen‐bond‐donor capabilities of methanol compared to water. The importance of the solvent contribution to the IR shift, as well as the significantly different hydrogen formation capabilities of water and methanol, makes the amide I band sensitive to composition changes in the local environment close to the peptide/solvent interface. This allows, in principle, an experimental determination of the composition of the solvent in close proximity to the peptide surface. For the AK peptide case, we observe at low methanol concentrations a significantly enhanced methanol concentration at the peptide/solvent interface, supposedly promoted by the partially hydrophobic character of the AK peptide’s solvent‐accessible surface.     

Theoretical Prediction of Substituent Effects on the Intrinsic Folding Properties of β‐Peptides

A systematic conformational analysis on blocked β‐amino acids as constituents of β‐peptides by ab initio MO theory reveals that the conformer pool of β‐peptide monomers is essentially determined by the conformation of simple submonomer fragments. The influence of single and multiple substitutions at the C(α) and C(β) backbone atoms on the intrinsic folding properties of the monomers was estimated both in the single‐molecule approximation and in a polar solvent continuum, applying a quantum‐chemical SCRF model. Substitution at C(β) has a higher impact on the β‐amino acid conformation than a substitution at C(α). It can be shown that the conformations of important periodic secondary structures in β‐peptides belong to the conformer pool of the monomers, even for those secondary‐structure elements where H‐bond formation appears only in longer sequences. Rules for design of special secondary‐structure types by selection of an actual substituent pattern in the β‐amino acid constituents have been derived within the monomer approach.     

Effect of solvent on absorption and fluorescence spectra of a typical fluorinated azo dye for its acidic and basic structures

The effect of 15 polar solvents on absorption and fluorescence energies of a typical fluorinated azo dye, 4-(2,3,5,6-tetrafluoro-pyridin-4-yl azo)-phenol, was reported for its acidic, MH, and basic, M, structures.For MH, the absorption energy is described on the basis of multi-linear equation with Taft's π* (solvent polarity) and β (hydrogen bond acceptor) parameters while the fluorescence energy varies rectilinearly with free energy of transferring the proton to the surrounding solvent, ΔG_t°.For M, the hydrogen bonding donor ability of protic solvent, α, is a predominant factor which affects the absorption energy while in aprotic solvents, the absorption energy correlates linearly with Kirkwood function. As the ability of the solvent for hydrogen bonding increases, the absorption band width will increase in parallel with the transition energy.     

Molecular Dynamics Simulations of a β-Hairpin Fragment of Protein G by Means of Atom-Bond Electronegativity Equalization Method Fused into Molecular Mechanics (ABEEMσπ/MM)

There are some controversial opinions about the origin of folding β‐hairpin stability in aqueous solution. In this study, the structural and dynamic behavior of a 16‐residue β‐hairpin from B1 domain of protein G has been investigated at 280, 300, 350 and 450 K using molecular dynamics (MD) simulations by means of Atom‐Bond Electronegativity Equalization Method Fused into Molecular Mechanics i.e., ABEEMδπ/MM and the explicit ABEEM‐7P water solvent model. In addition, a 300 K simulation of one mutant having the aromatic residues substituted with alanines has been performed. The hydrophobic surface area, hydrophilic surface area and some structural properties have been used to measure the role of the hydrophobic interactions. It is found that the aromatic residues substituted with alanines have shown an evident destabilization of the structure and unfolding started after 1.5 ns. It is also found that the number of the main chain hydrogen bonds have different distributions through three different simulations. All above demonstrate that the hydrophobic interactions and the main chain hydrogen bonds play an important role in the stability of the folding structure of β‐hairpin in solution. Furthermore, through the structural analyses of the β‐hairpin structures from four temperature simulations and the comparison with other MD simulations of β‐hairpin peptides, the new ABEEMδπ force field can reproduce the structural data in good agreement with the experimental data.     

Designed Beta‐Turn Mimic Based on the Allylic‐Strain Concept: Evaluation of Structural and Biological Features by Incorporation into a Cyclic RGD Peptide (Cyclo(‐L‐arginylglycyl‐L‐α‐aspartyl‐))

The (3R,5S,6E,8S,10R)‐11‐amino‐3,5,8,10‐tetramethylundec‐6‐enoic acid (ATUA; 1 ), which was designed as a βII′‐turn mimic according to the concepts of allylic strain and 2,4‐dimethylpentane units, was incorporated into a cyclic RGD peptide. The three‐dimensional structure of cyclo(‐RGD‐ATUA‐) (=cyclo(‐Arg‐Gly‐Asp‐ATUA‐)) 4 in H₂O was determined by NMR techniques, distance geometry calculations and molecular‐dynamics simulations. The RGD sequence of 4 shows high conformational flexibility but some preference for an extended conformation. The structural features of the RGD sequence of 4 were compared with the RGD moiety of cyclo(‐RGDfV‐) (=cyclo(‐Arg‐Gly‐Asp‐D ‐Phe‐Val‐)). In contrast to cyclo(‐RGDfV‐), which is a highly active αvβ3 antagonist and selective against αIIbβ3, cyclo(‐RGD‐ATUA‐) shows a lower activity and selectivity. The structure of the ATUA residue in the cyclic peptide resembles a βII′‐turn‐like conformation. Its middle part, adjacent to the C?C bond, strongly prefers the designed and desired structure.     

Solvent‐Modulated Influence of Intramolecular Hydrogen‐Bonding on the Conformational Properties of the Hydroxymethyl Group in Glucose and Galactose: A Molecular Dynamics Simulation Study

Intramolecular hydrogen‐bonding (H‐bonding) is commonly regarded as a major determinant of the conformation of (bio)molecules. However, in an aqueous environment, solvent‐exposed H‐bonds are likely to represent only a marginal (possibly adverse) conformational driving as well as steering force. For example, the hydroxymethyl rotamers of glucose and galactose permitting the formation of an intramolecular H‐bond with the adjacent hydroxyl group are not favored in water but, in the opposite, least populated. This is because the solvent‐exposed H‐bond is dielectrically screened as well as subject to intense H‐bonding competition by the water molecules. In the present study, the effect of a decrease in the solvent polarity on this rotameric equilibrium is probed using molecular dynamics simulation. This is done by considering six physical solvents (H₂O, DMSO , MeOH , CHC l₃, CC l₄, and vacuum), along with 19 artificial water‐like solvent models for which the dielectric permittivity and H‐bonding capacity can be modulated independently via a scaling of the O–H distance and of the atomic partial charges. In the high polarity solvents, the intramolecular H‐bond is observed, but arises as an opportunistic consequence of the proximity of the H‐bonding partners in a given rotameric state. Only when the polarity of the solvent is decreased does the intramolecular H‐bond start to induce a conformational pressure on the rotameric equilibrium. The artificial solvent series also reveals that the effects of the solvent permittivity and of its H‐bonding capacity mutually enhance each other, with a slightly larger influence of the permittivity. The hydroxymethyl conformation in hexopyranoses appears to be particularly sensitive to solvent‐polarity effects because the H‐bond involving the hydroxymethyl group is only one out of up to five H‐bonds capable of forming a network around the ring.     

Stability and Unfolding Mechanism of the N‐terminal β‐Hairpin from [2Fe‐2S] Ferredoxin I by Molecular Dynamics Simulations

The stability and unfolding mechanism of the N‐terminal β‐hairpin of the [2Fe‐2S] ferredoxin I from the blue‐green alga Aphanothece sacrum in pure methanol, 40% (v/v) methanol‐water, and pure water systems were investigated by 10 ns molecular dynamics simulations under periodic boundary conditions. The β‐hairpin was mostly in its native‐like state in pure methanol, whereas it unfolds dramatically following the ‘zip‐up’ mechanism when it was placed in pure water. Both interstrand and inside‐turn hydrogen bonds account for the stability of the β‐hairpin in its native‐like conformation, whereas hydrophobic interactions among nonpolar side chains are responsible for maintaining its stable loop‐like intermediate structures in 40% (v/v) methanol‐water. Reducing solvent polarity seems to increase the stability of the β‐hairpin in its native‐like structure. Methanol is likely to mimic the partially hydrophobic environment around the N‐terminal β‐hairpin by the subsequent α‐helix.     

Morphology study of Nafion membranes prepared by solutions casting

The structures of Nafion membranes prepared by solutions casting from low aliphatic alcohols/water mixture solvents and N,N′‐dimethyl formamide (DMF) solvent were investigated using differential scanning calorimeter and small angle X‐ray scattering. The aggregation behavior of Nafion molecules in the casting solutions was also investigated using dynamic light scattering. We show that the morphology of membranes was strongly influenced by the conformations of Nafion molecules in the solutions. In aliphatic alcohol/water mixture solvents, which have a worse compatibility with Nafion backbones, the Nafion molecules aggregate and form fringed rod‐like structures. These primary rod‐like structures then aggregate again through fringed side chains to form secondary ionic aggregations. In DMF solvent, owing to its better compatibility with Nafion backbones, less Nafion molecules aggregate. The high degree of Nafion molecular aggregations in aliphatic alcohol/water mixture solvents leads to a high degree of hydrophobic and hydrophilic phase separation for membranes prepared by casting from Nafion/aliphatic alcohol/water solutions. However, the lower degree of molecular aggregations in DMF solvent results in a lower degree of hydrophobic and hydrophilic phase separation for membranes prepared by casting from Nafion/DMF solution. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 3044–3057, 2005     

On the Use of a Supramolecular Coarse‐Grained Model for the Solvent in Simulations of the Folding Equilibrium of an Octa‐β‐peptide in MeOH and H2O

Molecular dynamics (MD) simulation can give a detailed picture of conformational equilibria of biomolecules, but it is only reliable if the force field used in the simulation is accurate, and the sampling of the conformational space accessible to the biomolecule shows many (un)folding transitions to allow for precise averages of observable quantities. Here, the use of coarse‐grained (CG) solvent MeOH and H₂O models to speed up the sampling of the conformational equilibria of an octa‐β‐peptide is investigated. This peptide is thought to predominantly adopt a 3₁₄‐helical fold when solvated in MeOH, and a hairpin fold when solvated in H₂O on the basis of the NMR data. Various factors such as the chirality of a residue, a force‐field modification for the solute, coarse‐graining of the solvent model, and an extension of the nonbonded interaction cut‐off radius are shown to influence the simulated conformational equilibria and the agreement with the experimental NMR data for the octa‐β‐peptide.     

Validation of the GROMOS 54A7 Force Field Regarding Mixed α/β‐Peptide Molecules

A molecular‐dynamics (MD) simulation study of two heptapeptides containing α‐ and β‐amino acid residues is presented. According to NMR experiments, the two peptides differ in dominant fold when solvated in MeOH: peptide 3 adopts predominantly β‐hairpin‐like conformations, while peptide 8 adopts a 14/15‐helical fold. The MD simulations largely reproduce the experimental data. Application of NOE atom? atom distance restraining improves the agreement with experimental data, but reduces the conformational sampling. Peptide 3 shows a variety of conformations, while still agreeing with the NOE and ³J‐coupling data, whereas the conformational ensemble of peptide 8 is dominated by one helical conformation. The results confirm the suitability of the GROMOS 54A7 force field for simulation or structure refinement of mixed α/β‐peptides in MeOH.     

β‐Hairpins Generated from Hybrid Peptide Sequences Containing both α‐ and β‐Amino Acids

The incorporation of the β‐amino acid residues into specific positions in the strands and β‐turn segments of peptide hairpins is being systematically explored. The presence of an additional torsion variable about the C(α) C(β) bond (θ) enhances the conformational repertoire in β‐residues. The conformational analysis of three designed peptide hairpins composed of α/β‐hybrid segments is described: Boc‐Leu‐Val‐Val‐^DPro‐β Phe ‐Leu‐Val‐Val‐OMe ( 1 ), Boc‐Leu‐Val‐β Val ‐^DPro‐Gly‐β Leu ‐Val‐Val‐OMe ( 2 ), and Boc‐Leu‐Val‐β Phe ‐Val‐^DPro‐Gly‐Leu‐β Phe ‐Val‐Val‐OMe ( 3 ). 500‐MHz ¹H‐NMR Analysis supports a preponderance of β‐hairpin conformation in solution for all three peptides, with critical cross‐strand NOEs providing evidence for the proposed structures. The crystal structure of peptide 2 reveals a β‐hairpin conformation with two β‐residues occupying facing, non‐H‐bonded positions in antiparallel β‐strands. Notably, βVal(3) adopts a gauche conformation about the C(α) C(β) bond (θ=+65°) without disturbing cross‐strand H‐bonding. The crystal structure of 2 , together with previously published crystal structures of peptides 3 and Boc‐β Phe ‐β Phe ‐^DPro‐Gly‐β Phe ‐β Phe ‐OMe, provide an opportunity to visualize the packing of peptide sheets with local ‘polar segments' formed as a consequence of reversal peptide‐bond orientation. The available structural evidence for hairpins suggests that β‐residues can be accommodated into nucleating turn segments and into both the H‐bonding and non‐H‐bonding positions on the strands.     

Conformational Stability of Bovine Serum Albumin in Aqueous Amides: A Further Insight into the Mechanism of Urea Acting on the Protein

The binding distances of fluorescein to bovine serum albumin (BSA) in formamide‐water and N,N‐dimethyl‐ formamide‐water mixtures were determined by fluorescence quenching method and compared with the values in urea‐water mixtures in our previous work. The results, together with the analysis of fluorescence spectra, were utilized to probe the conformational stability of protein in aqueous amides, providing a further insight into the mechanism of urea acting on protein. The spectral properties of BSA showed significant difference in the aqueous solutions of the three kinds of amide and indicated that both NH₂ group and C=O group could form hydrogen bond with the protein, serving as donor and acceptor, respectively. However, the results revealed that the multiple hydrogen bonds of NH₂ group with back bond and hydrophilic side chains of the protein played a key role in the nonspecific urea‐mediated network of intramolecular interaction due to its higher hydrogen bonding capability compared to C=O group.     

Tuning One‐Dimensional Nanostructures of Bola‐Like Peptide Amphiphiles by Varying the Hydrophilic Amino Acids

By combining experimental measurements and computer simulations, we here show that for the bola‐like peptide amphiphiles XI₄X, where X=K, R, and H, the hydrophilic amino acid substitutions have little effect on the β‐sheet hydrogen‐bonding between peptide backbones. Whereas all of the peptides self‐assemble into one dimensional (1D) nanostructures with completely different morphologies, that is, nanotubes and helical nanoribbons for KI₄K, flat and multilayered nanoribbons for HI₄H, and twisted and bilayered nanoribbons for RI₄R. These different 1D morphologies can be explained by the distinct stacking degrees and modes of the three peptide β‐sheets along the x‐direction (width) and the z‐direction (height), which microscopically originate from the hydrogen‐bonding ability of the sheets to solvent molecules and the pairing of hydrophilic amino acid side chains between β‐sheet monolayers through stacking interactions and hydrogen bonding. These different 1D nanostructures have distinct surface chemistry and functions, with great potential in various applications exploiting the respective properties of these hydrophilic amino acids.     

Atomistic insights on the LCST behavior of PMEO2MA in water by molecular dynamics simulations

Fully atomistic molecular dynamics simulations of poly(2‐[2‐methoxyethoxy]ethyl methacrylate) (PMEO₂MA) in water at temperatures below and above its lower critical solution temperature (LCST) were performed to improve the understanding of its LCST behavior. Atomic trajectories were used to calculate various structural and dynamic properties. Simulation results show that PMEO₂MA undergo a distinct coil‐to‐globule transition above LCST. Detailed analyses of the number of first hydration shell water molecules around various atomic regions are revealed that the water solubility of PMEO₂MA below LCST is mainly provided by the hydrophobic hydration around the side chain carbon atoms. This is achieved by the cage‐like water network formations which are disrupted when the temperature is increased above LCST, accompanied by significant amount of water molecule release and local water‐ordering reduction, which leads to the LCST phase transition. Furthermore, other analyses such as the number of hydrogen bonds and hydrogen bond lifetimes suggest that intermolecular hydrogen bondings between polymer and water molecules have little effect on the phase transition. Our results will contribute to a better understanding on the LCST phase transition of oligo(ethylene glycol) methyl ether methacrylate (OEGMA)‐based homopolymers at atomistic level that will be useful when designing homo‐ and co‐polymers of OEGMAs with desired properties. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2018 , 56, 429–441     

Para‐linked and meta‐linked cationic water‐soluble fluorene‐containing poly(aryleneethynylene)s: Conformational changes and their effects on iron–sulfur protein detection

Four para‐linked or meta‐linked cationic water‐soluble fluorene‐containing poly(aryleneethynylene)s (PAEs) were synthesized to investigate the solvent‐induced π‐stacked self‐assembly. These PAE backbones are composed of fluorenylene and phenylene units, which are alternatively linked by ethynylene bonds. UV–vis absorption and photoluminescence spectra were used to study their conformational changes as solvent was gradually changed from MeOH to H₂O. In pure water, with gradually increased meta‐phenylene content (0, 50, and 100%), they underwent a gradual transition process of conformation from disordered aggregate structure to helix structure, which was not compactly folded. Moreover, the polymer with an ammonium‐functionalized side chain on the meta‐phenylene unit appeared to adopt a more incompact or extended helix conformation than the corresponding one without this side chain. Furthermore, the conformational changes of these cationic PAEs in H₂O were used to study their effects on biological detection. Rubredoxin (Rd), a type of anionic iron–sulfur‐based electron transfer protein, was chosen to act as biological analyte in the fluorescence quenching experiments of these polymers. Preliminary results suggest that they all exhibit amplified fluorescence quenching, and that the polymer with more features of helix conformation tends to be quenched by Rd more efficiently. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 5424–5437, 2006