Formation Of Helical Structure Research Articles

Insertion into lipid bilayer of truncated pHLIP®peptide

The investigation of pH-dependent membrane-associated folding has both fundamental interest and practical applications for targeting of acidic tumors and specific delivery of therapeutic molecules across membrane of cancer cells. We and others investigated molecular mechanism and medical uses of class of water soluble membrane peptides, pH (Low) Insertion Peptides (pHLIP® peptides). Here we employed optical spectroscopy methods to study interactions of the truncated pHLIP® peptide (Short pHLIP®) with lipid bilayer of membrane. Tryptophan fluorescence, CD and OCD data indicate on pH-triggered formation of transmembrane helical structure. Dual quenching and FRET assays demonstrated that Short pHLIP® peptide spans lipid bilayer of membrane similar to Long pHLIP® peptides. Truncated pHLIP® peptides with multiple charged and protonatable residues in their sequences potentially can make these peptides to be less hydrophobic compared to Long pHLIP® peptides, and might have utility in tumor imaging, and potentially, in pH-regulated cytoplasmic delivery of moderately hydrophobic drugs.

Numerical simulation of a helical shape electric arc in the external axial magnetic field

Within the frameworks of non-stationary three-dimensional mathematical model, in approximation of a partial local thermodynamic equilibrium, a numerical calculation was made of characteristics of DC electric arc burning in a cylindrical channel in the uniform external axial magnetic field. The method of numerical simulation of the arc of helical shape in a uniform external axial magnetic field was proposed. This method consists in that that in the computational algorithm, a “scheme” analog of fluctuations for electrons temperature is supplemented. The “scheme” analogue of fluctuations increases a weak numerical asymmetry of electrons temperature distribution, which occurs randomly in the course of computing. This asymmetry can be “picked up” by the external magnetic field that continues to increase up to a certain value, which is sufficient for the formation of helical structure of the arc column. In the absence of fluctuations in the computational algorithm, the arc column in the external axial magnetic field maintains cylindrical axial symmetry, and a helical form of the arc is not observed.

Characterizing the structural and folding properties of long‐sequence hypomurocin B peptides and their analogs

We studied the folding processes of long-sequence hypomurocin (HM) peptides and their analogs by means of molecular dynamics methods, focusing on the formation of various helical structures and intramolecular H-bonds. The evolution of different helical conformations, such as the 310 -, α-, and left-handed α-helices, was examined, taking into account the entire sequence and each amino acid of peptides. The results indicated that the HM peptides and their analogs possessed a propensity to adopt helical conformations, and they showed a preference for the 310 -helical structure over the α-helical one. The evolution of a variety of the intramolecular H-bonds, including local and non-local interactions, was also investigated. The results pointed out that on the one hand, the appearance of local, helix-stabilizing H-bonds correlated with the presence of helical conformations, and on the other hand, the non-local H-bonds did not affect significantly the formation of helical structures. Additionally, comparing the structural and folding features of HM peptides and their analogs, our study led to the observation that the L-D isomerism of isovaline amino acid induced effects on the folding processes of these long-sequence peptaibol molecules. Accordingly, the HM peptides and their analogs could be characterized by typical structural and folding properties. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 645-657, 2016.

Significance of bending restraints for the stability of helical polymer conformations.

We performed parallel-tempering Monte Carlo simulations to investigate the formation and stability of helical tertiary structures for flexible and semiflexible polymers, employing a generic coarse-grained model. Structural conformations exhibit helical order with tertiary ordering into single helices, multiple helical segments organized into bundles, and disorganized helical arrangements. For both bending-restrained semiflexible and bending-unrestrained flexible helical polymers, the stability of the structural phases is discussed systematically by means of hyperphase diagrams parametrized by suitable order parameters, temperature, and torsion strength. This exploration lends insight into the restricted flexibility of biological polymers such as double-stranded DNA and proteins.

Reduced and mutant lysozyme refolding with lipid vesicles. Model study of disulfide impact on equilibria and dynamics

The recovery of secondary structure in disordered, disulfide-reduced hen egg white lysozyme (HEWL) upon interaction with lipid vesicles was studied using circular dichroism (CD), fluorescence and infrared (IR) spectroscopic techniques. Lipid vesicles having negative head groups, such as DMPG, interact with reduced HEWL to induce formation of more helical structure than in native HEWL, but no stable tertiary structure was evident. Changes in tertiary structure, as evidenced by local environment of the tryptophan residues, were monitored by fluorescence. Spectra for oxidized HEWL, reduced HEWL and mutants with no or just one disulfide bond developed variable degrees of increased helicity when added to negatively charged lipid vesicles, mostly depending on packing of tails. When mixed with zwitterionic lipid vesicles, reduced HEWL developed β-sheet structure with no change in helicity, indicating an altered interaction mechanism. Stopped flow CD and fluorescence dynamics, were fit to multi-exponential forms, consistent with refolding to metastable intermediates of increasing helicity for HEWL interacting with lipid vesicles. Formation of an intermediate after rapid interaction of the lipid vesicles and the protein is supported by the correlation of faster steps in CD and fluorescence kinetics, and largely appears driven by electrostatic interaction. In subsequent slower steps, the partially refolded intermediate further alters structure, gaining helicity and modifying tryptophan packing, as driven by hydrophobic interactions.

Assembly of an Achiral Chromophore into Light-Responsive Helical Nanostructures in the Absence of Chiral Components.

The chirality found in living organisms is one of unsolved mysteries on Earth. It is crucial to understand the manner in which small achiral molecules evolve into helical superstructures in the absence of chiral components because this process can provide important insights regarding the origin of chirality in nature. 1) the uncommon helical assembly of an achiral trigonal chromophore into helical nanostructures with aggregation-induced emission enhancement (AIEE) characteristics and 2) the tunability of the helical pitch and fluorescence intensity in response to light is reported. The Rietveld refinement of X-ray diffraction (XRD) patterns and the growth process suggest that a striking transformation from an achiral to an asymmetric molecule can occur as a result of specific interactions with certain solvents, presumably leading to the unique helical assembly. More importantly, exposure to UV or visible light promoted not only the formation of irregular helical structures with a wide range of pitch lengths but also an increase in fluorescence intensity.

The Role of Calcium on the Active Site of Snake Venom Phospholipase A2: Molecular Dynamics Simulations

Snake venoms are rich in phospholipase A2 (PLA2) and their hydrolysis of cell membrane phospholipids explains the role of the enzyme in venom toxicity. Calcium is known to plays important role at the active site of PLA2 during catalysis. In this study, molecular dynamics simulations of free PLA2 and calcium bound PLA2 were carried out using GROMACS 4.5.5 to evaluate the role of calcium in PLA2 catalysis. The results showed that calcium induced formation of helical structures between Arg62 - Lys66, Asn107 - Tyr111 and Asp114 - Cys119 in PLA2 which with time disappeared through the formation and opening of loops. Calcium induced atomistic movements and conformational changes in snake venom PLA2 which led to the formation of a widened cleft at the active site of calcium bound PLA2 when compared with free PLA2. This could lead to a better binding and accommodation of substrate, thus enhancing catalysis. This study confirms the role of calcium towards the action of PLA2 in snake venom toxicity and could provide useful information for the design of small molecules that can function as PLA2 inhibitors.

Studying the structural and folding features of long-sequence trichobrachin peptides.

In this theoretical study, the folding processes of long-sequence trichobrachin peptides (i.e., TB IIb peptides) were investigated by molecular dynamics methods. The formation of various helical structures (i.e., 310 -, α-, and left-handed α-helices) was studied with regard to the entire sequence of peptides, as well as to each amino acid. The results pointed out that TB IIb molecules showed a propensity to form helical conformations, and they could be characterized by 310 -helical structure rather than by α-helical structure. The formation of local (i.e., i←i+3 and i←i+4) as well as of non-local (i.e., i←i+n, where n>4; and all i→i+n) H-bonds was also examined. The results revealed that the occurrence of local, helix-stabilizing H-bonds was in agreement with the appearance of helical conformations, and the non-local H-bonds did not produce relevant effects on the evolution of helical structures. Based on the data obtained by our structural investigation, differences were observed between the TB IIb peptides, according to the type of amino acid located in the 17th position of their sequences. In summary, the folding processes were explored for TB IIb molecules, and our theoretical study led to the conclusion that these long-sequence peptaibols showed characteristic structural and folding features.

Cotranslational Protein Folding inside the Ribosome Exit Tunnel.

SummaryAt what point during translation do proteins fold? It is well established that proteins can fold cotranslationally outside the ribosome exit tunnel, whereas studies of folding inside the exit tunnel have so far detected only the formation of helical secondary structure and collapsed or partially structured folding intermediates. Here, using a combination of cotranslational nascent chain force measurements, inter-subunit fluorescence resonance energy transfer studies on single translating ribosomes, molecular dynamics simulations, and cryoelectron microscopy, we show that a small zinc-finger domain protein can fold deep inside the vestibule of the ribosome exit tunnel. Thus, for small protein domains, the ribosome itself can provide the kind of sheltered folding environment that chaperones provide for larger proteins.

Hierarchical nanostructures self-assembled from a mixture system containing rod-coil block copolymers and rigid homopolymers.

Self-assembly behavior of a mixture system containing rod-coil block copolymers and rigid homopolymers was investigated by using Brownian dynamics simulations. The morphologies of formed hierarchical self-assemblies were found to be dependent on the Lennard-Jones (LJ) interaction εRR between rod blocks, lengths of rod and coil blocks in copolymer, and mixture ratio of block copolymers to homopolymers. As the εRR value decreases, the self-assembled structures of mixtures are transformed from an abacus-like structure to a helical structure, to a plain fiber, and finally are broken into unimers. The order parameter of rod blocks was calculated to confirm the structure transition. Through varying the length of rod and coil blocks, the regions of thermodynamic stability of abacus, helix, plain fiber, and unimers were mapped. Moreover, it was discovered that two levels of rod block ordering exist in the helices. The block copolymers are helically wrapped on the homopolymer bundles to form helical string, while the rod blocks are twistingly packed inside the string. In addition, the simulation results are in good agreement with experimental observations. The present work reveals the mechanism behind the formation of helical (experimentally super-helical) structures and may provide useful information for design and preparation of the complex structures.

Development of Electrochemical and Optical Based Biosensors

During recent years, rapid and highly selective determination of nucleic acid (in particularly, DNA) has gained much importance in the field of disease diagnostics, gene analysis, tissue matching, forensic and environmental protection. Various techniques have been employed for DNA detection like fluorescence, surface plasmon resonance (SPR), quartz crystal microbalance (QCM), piezoelectric, electroluminiscene, and electro-chemical. Among all these techniques, electro chemical and SPR based biosensors for nucleic acid detection have attracted researchers worldwide due to their high sensitivity, low detection limit, fast response time, wide detection range, good reliability, easy handling and portability. DNA based biosensors rely on the immobilization of a single-stranded oligonucleotide probe onto a surface to recognize by hybridization its complementary target sequence. The probes are typically short oligonucleotides that are capable of hybridizing with specific and unique regions of the target nucleotide sequence. Due to formation of double helical structure between complementary strands, a change in current or SPR angle could be easily observed. In the present study, an effort has been made towards the development of ZnO matrix based biosensors for the detection of Meningitidis using electrochemical (Amperometric) and SPR techniques. The surface plasmon modes have been excited at the ZnO-gold interface in the Kretschmann configuration using a right angled BK7 glass prism (np =1.517) with the help of a laboratory assembled system. The shift in SPR reflectance curve for increasing concentration of target DNA ranging from 10 to180 ng/μl were recorded which shows the promising application of SPR technique towards biosensing. The Sensitivity of the ZnO thin film using SPR is found to be about 0.031°/(ng/μl) with the minimum detection limit of 5 ng/μl. Zinc oxide nanostructures possessing flower-like morphology have been synthesized onto platinized silicon substrate by simple and economical hydrothermal method. The electrochemical sensing response behaviour of the DNA bioelectrode (ssth-DNA/ ZNF/Pt/Si) has been studied by both differential pulse voltammetric (DPV) as well as impedimetric techniques. The fabricated DNA biosensor can quantify wide range of the complementary targets sth-DNA in the range 5–240 ng/μl with good linearity (R=0.98), high sensitivity (168.64μAng/μl/cm2) and low detection limit of about 5ng/μl.

Mechanisms of Folding upon Binding

Investigating families of intrinsically disordered proteins that fold upon binding. 
 One particularly useful approach for investigating protein folding is 'to investigate the folding of several topologically, structurally and/or evolutionarily related proteins in order to discern patterns and trends in folding (stability, pathways and mechanisms). We are now applying this approach to the folding of intrinsically disordered proteins.
 The systems we are studying all involve formation of helical structure when a disordered protein binds its target. The properties of these systems are vastly different, binding affinity ranges from µM – nM and association and disassociation rate constants vary by many orders of magnitude. This brings different challenges for determining the kinetics of assembly and disassembly.
 We are investigating some fundamental questions in the IDP field: How important is residual structure in the IDP‾ How do regions outside the binding site influence binding‾ What are the mechanisms of binding‾ What role does the partner protein play in determining the binding mechanism and the strength of binding‾ Can we relate biophysical properties to specific IDP functions‾
 I will discuss our latest findings.

Residual Stresses and Poisson’s Effect Drive Shape Formation and Transition of Helical Structures

Residual Stresses and Poisson’s Effect Drive Shape Formation and Transition of Helical Structures

Fast helix formation in the B domain of protein A revealed by site-specific infrared probes.

Comparison of experimental and computational protein folding studies can be difficult because of differences in structural resolution. Isotope-edited infrared spectroscopy offers a direct measure of structural changes involved in protein folding at the single-residue level. Here we demonstrate the increased resolution of site-specific infrared probes to the peptide backbone in the B domain of staphylococcal protein A (BdpA). (13)C═(18)O-labeled methionine was incorporated into each of the helices using recombinant protein expression. Laser-induced temperature jumps coupled with infrared spectroscopy were used to probe changes in the peptide backbone on the submillisecond time scale. The relaxation kinetics of the buried helices, solvated helices, and labeled positions were measured independently by probing the corresponding bands assigned in the amide I region. Using these wavelength-dependent measurements, we observe a fast nanosecond phase and slower microsecond phase at each position. We find at least partial formation of helices 1-3 in the fast intermediate state that precedes the transition state. These measurements provide direct, time-resolved experimental evidence of the early formation of partial helical structure in helices 1 and 3, supporting folding models proposed by computer simulations.

Self-assembly and gelation of poly(aryl ether) dendrons containing hydrazide units: factors controlling the formation of helical structures.

Self-assembly of AB2 and AB3 type low molecular weight poly(aryl ether) dendrons that contain hydrazide units were used to investigate mechanistic aspects of helical structure formation during self-assembly. The results suggest that there are three important aspects that control helical structure formation in such systems with acyl hydrazide/hydrazone linkage: i) J-type aggregation, ii) the hydrogen-bond donor/acceptor ability of the solvent, and iii) the dielectric constant of the solvent. The monomer units self-assemble to form dimer structures through hydrogen-bonding and further assembly of the hydrogen-bonded dimers leads to macroscopic chirality in the present case. Dimer formation was confirmed by NMR spectroscopy and by mass spectrometry. The self-assembly in the system was driven by hydrogen-bonding and π-π stacking interactions. The morphology of the aggregates formed was examined by scanning electron microscopy, and the analysis suggests that aprotic solvent systems facilitate helical fibre formation, whereas introduction of protic solvents results in the formation of flat ribbons. This detailed mechanistic study suggests that the self-assembly follows a nucleation-elongation model to form helical structures, rather than the isodesmic model.

Racemic and conglomerate 1-(4-haloaryl)ethylammonium tetrachlorocobaltate salts: formation of helical structures

Whereas rac-1-(4-fluorophenyl)ethylamine (rac-fpea) reacts with CoCl2 and HCl forming rac-[(R)-fpeaH]2[CoCl4], the chloro analogue rac-1-(4-chlorophenyl)ethylamine (rac-cpea) yields a conglomerate of [(R)-cpeaH]3[CoCl4]Cl and [(S)-cpeaH]3[CoCl4]Cl.

The Effect of Surface Adsorption on Tertiary Structure Formation in Helical Polymers

Formation of tertiary structures made up of helical polymer segments is modified by the introduction of a substrate on which the polymer is adsorbed. The effect of a substrate on biological systems such as helical structures may have been important in the formation of early life. We perform replica-exchange Monte Carlo simulations to study this effect on formation of helical structures in corse grained polymers – comparing the structural phase space for both adsorbed and non-adsorbed helical polymers. For this purpose a generic, hybrid coarse-grained model for polymer adsorption has been employed.

Ordered structures of nanorods induced by the helixes of semiflexible polymer chains

Self-assembly of nanoparticles, such as nanospheres, nanorods (NRs), and nanotubes, in polymer systems is one of the most prominent and promising candidates for the development of novel materials with high mechanical, optical, and electrical performances. A most concerned topic on the nanoparticle/polymer composites is the spatial arrangement and distribution of nanoparticles in the nanocomposites, which is controlled by the competition between the entropic packing constraints related to the incompatibility between species with different sizes and geometries, and the enthalpic consequences of a variety of polymer-nanoparticle interactions. The studies on the nonspherical nanoparticles, such as NRs, are of more challenging than on spherical nanoparticles, because both positional and orientational ordering of anisotropic nanoinclusion have an important influence on the morphology of nanocomposition, while those studies are necessary for applications of nanoscopic anisotropic objects in photovoltaic and filled emission devices. When low-volume fractions of NRs are immersed in a binary, phase-separating blend, the rods can self-assemble into needle-like, percolating networks and this special structure can enhance the macroscopic electrical conductivity and mechanical property of the material. When an electric field is applied, the phase separations of ligand-functionalized NRs in a polymer matrix and densely packed hexagonal arrays of NRs are produced. In this paper, by employing the coarse-grained model and molecular dynamics simulation, we explore the structures of nanocomposites in which a small number of NRs bind with semiflexible polymer chain. The morphology of NRs/polymer mixture is greatly affected by the bending energy b of semiflexible polymer and the binding energy D0 between NRs and semiflexible polymer. If the binding energy D0 is less than 1.1kBT, the NRs are almost free and a gas-like phase is observed. For a suitably large value of D0, three completely different morphologies of NRs/polymer mixtures are identified, namely, the side-to-side parallel aggregation of NRs, the end-to-end parallel aggregation of NRs, and the dispersion of NRs. For the flexible polymer chain (i.e., small bending energy b), the sideto- side parallel aggregation structure of NRs and the disordered conformation of adsorbed polymer chain are observed. In general, a typical equilibrium conformation of free flexible polymer chain is random coil, the binding energy between NRs and polymer can lead to the collapse of a random coil for flexible polymer chain, and the NRs aggregate in the manner of the side-to-side parallel to each other because the enthalpy is maximized through sharing the more polymer monomers between neighbor NRs. That is to say, the local aggregation of NRs can be found because the orientational entropy can make the aggregated NRs arrange in the side-to-side parallel manner. In the rigid polymer chain limit (very large bending energy), the rigid polymer chain is stretched and the NRs are well dispersed. As the rigid polymer holds a long persistence length, the NRs can move freely along the stretched polymer chain, and the dispersed conformation of NRs is formed. For the semiflexible polymer chain with a moderate bending energy, the NRs are aggregated in the end-to-end parallel arrangement. Meanwhile, the polymer monomers wrap around those NRs in a well-defined helical structure. The above discussion indicates that the morphologies of NRs are closely related to the conformations of polymer chains. In fact, when a semiflexible polymer chain binds with a large rigid surface, such as nanotube, the helical structure will be formed and it is driven by entropy. The formation of helical structures for a semiflexible polymer chain can induce NRs to form an end-to-end parallel aggregation. The formation of end-to-end parallel arrangement of NR aggregation is driven by the helical structure of semiflexible polymer chain. For the moderate binding energy, the entropy can drive the semiflexible polymer chain to form local helical structure around the NRs. When more NRs are added to the semiflexble polymer chain/NR mixtures, more local helical structures around NRs are formed. Because the movements of NRs binding with the semiflexible chain are nearly free and an end-to-end parallel arrangement of NRs can form more helical structures than the dispersed NRs, the self-assembly of NRs into an end-to-end parallel structure is expected. That is to say, the formation of end-to-end parallel aggregation of NRs is induced by the helix of semiflexible polymers because it can gain more entropies. The self-assembly of a small number of NRs can be well controlled by varying the stiffness of adsorbed polymer chain. This investigation may provide a new pathway to develop smart medium to manipulate the aggreagtion behavior of a few NRs and to construct novel materials with high performance.

Spontaneous Helical Structure Formation in Laminin Nanofibers.

Laminin is a cross-shaped heterotrimer composed of three polypeptides chains that assembles into an insoluble extracellular matrix (ECM) network as part of the basement membrane, serving a vital role in many processes such as embryonic development, differentiation, and muscle and nerve regeneration. Here we engineered monodisperse laminin nanofibers using a surface-initiated assembly technique in order to investigate how changes in protein composition affect formation and structure of the network. Specifically, we compared laminin 111 with varying degrees of purity and with and without entactin to determine whether these changes alter biophysical properties. All the laminin types were reproducibly patterned as 200 μm long, 20 μm wide nanofibers that were successfuly released during surface-initiated assembly into solution. All nanofibers contracted upon release, and while initial lengths were identical, lengths of released fibers depended on the laminin type. Uniquely, the laminin 111 at high purity (>95%) and without entactin spontaneouly formed helical nanofibers at greater than 90%. Atomic force microscopy revealed that the nanofiber contraction was associated with a change in nanostructure from fibrillar to nodular, suggestive of refolding of laminin molecules into a globular-like conformation. Further, for the high purity laminin that formed helices, the density of the laminin at the edges of the nanofiber was higher than in the middle, providing a possible origin for the differential pre-stress driving the helix formation. Together, these results show that variation in the purity of laminin 111 and presence of entactin can have significant impact on the biophysical properties of the assembled protein networks. This highlights the fact that our understanding of protein assembly and function is still incomplete and that cell-free, in vitro assays can provide unique insights into the ECM.

Potential switchable circularly polarized luminescence from chiral cyclometalated platinum(II) complexes.

A series of chiral cyclometalated platinum(II) complexes, [Pt((−)-L1)(Dmpi)]Cl ((−)-1), [Pt((+)-L1)(Dmpi)]Cl ((+)-1), [Pt((−)-L2)(Dmpi)]Cl ((−)-2), [Pt((+)-L2)(Dmpi)]Cl ((+)-2), [Pt3((−)-L2)2(Dmpi)4](ClO4)4 ((−)-3), and [Pt3((+)-L2)2(Dmpi)4](ClO4)4 ((+)-3) [(−)-L1 = (−)-4,5-pinene-6′-phenyl-2,2′-bipyridine, (+)-L1 = (+)-4,5-pinene-6′-phenyl-2,2′-bipyridine), (−)-L2 = (−)-1,3-bis(2-(4,5-pinene)pyridyl)benzene, (+)-L2 = (+)-1,3-bis(2-(4,5-pinene)pyridyl)benzene, Dmpi = 2,6-dimethylphenyl isocyanide], have been designed and synthesized. In aqueous solutions, (−)-1 and (+)-1 aggregate into one-dimensional helical chain structures through Pt···Pt, π–π, and hydrophobic–hydrophobic interactions. (−)-3 and (+)-3 represent a novel helical structure with Pt–Pt bonds. The formation of helical structures results in enhanced and distinct chiroptical properties as evidenced by circular dichroism spectra. Circularly polarized luminescence (CPL) was observed from the aggregates of (−)-1 and (+)-1 in water, as well as (−)-3 and (+)-3 in dichloromethane. The CPL activity can be switched reversibly (for (−)-1 and (+)-1) or irreversibly (for (−)-3 and (+)-3) by varying the temperature.