Helix-coil Transition Research Articles

Transition on the entropic elasticity of DNA induced by intercalating molecules

We use optical tweezers to perform stretching experiments on DNA molecules when interacting with the drugs daunomycin and ethidium bromide, which intercalate the DNA molecule. Our results show that the persistence length of the DNA-drug complexes increases strongly as the drug concentration increases up to some critical value. Above this critical value, the persistence length decreases abruptly and remains approximately constant for larger drug concentrations, at least in the concentration range used in our experiments. Measured intercalators critical concentrations for the persistence length transition coincide with the reported values for the helix-coil transition of DNA-drug complexes obtained from sedimentation experiments. The contour length of the molecules increases monotonically and saturates as the drug concentration increases. The neighbor exclusion model fits to our results for the total drug concentration as a function of the relative increase of the contour length.

Structure of the Ebola Fusion Peptide in a Membrane-mimetic Environment and the Interaction with Lipid Rafts

The fusion peptide EBO(16) (GAAIGLAWIPYFGPAA) comprises the fusion domain of an internal sequence located in the envelope fusion glycoprotein (GP2) of the Ebola virus. This region interacts with the cellular membrane of the host and leads to membrane fusion. To gain insight into the mechanism of the peptide-membrane interaction and fusion, insertion of the peptide was modeled by experiments in which the tryptophan fluorescence and (1)H NMR were monitored in the presence of sodium dodecyl sulfate micelles or in the presence of detergent-resistant membrane fractions. In the presence of SDS micelles, EBO(16) undergoes a random coil-helix transition, showing a tendency to self-associate. The three-dimensional structure displays a 3(10)-helix in the central part of molecule, similar to the fusion peptides of many known membrane fusion proteins. Our results also reveal that EBO(16) can interact with detergent-resistant membrane fractions and strongly suggest that Trp-8 and Phe-12 are important for structure maintenance within the membrane bilayer. Replacement of tryptophan 8 with alanine (W8A) resulted in dramatic loss of helical structure, proving the importance of the aromatic ring in stabilizing the helix. Molecular dynamics studies of the interaction between the peptide and the target membrane also corroborated the crucial participation of these aromatic residues. The aromatic-aromatic interaction may provide a mechanism for the free energy coupling between random coil-helical transition and membrane anchoring. Our data shed light on the structural "domains" of fusion peptides and provide a clue for the development of a drug that might block the early steps of viral infection.

Reversible aggregation of gold nanoparticles induced by pH dependent conformational transitions of a self-assembled polypeptide

Controlling the stable structures of metallic nanoparticles on mesoscopic and macroscopic length scales is of great interest in nanotechnology. Here, this task is accomplished using a synthetic biopolymer that is responsive to external stimuli and undergoes changes in secondary structure. Reversible aggregation of gold nanoparticles (GNP) is induced by pH dependent changes in a self-assembled monolayer of disulfide modified poly( l-glutamic acid) (SSPLGA) with M w ∼ 27000 . The disulfide anchoring group drives chemisorption onto the gold nanoparticles and leads to the formation of a self-assembled monolayer. Characterization of the modified GNP and its aggregation behavior is performed using dynamic light scattering (DLS), UV–vis and IR spectroscopy, and transmission electron microscopy (TEM). Experimental results show that decrease in pH near 5.5 leads to aggregation of the modified GNP. The change in aggregation behavior with pH occurs within minutes, is reversible, and happens within a narrow range of pH from about 4.5 to 5.5. Comparison with literature data on molar enthalpy of hydrogen bonding, specific optical rotation, and ionization for the helix–coil transition of PLGA indicates that the aggregation of the SSPLGA modified GNP corresponds to the transition in the secondary structure of the polyacid.

Effect of cesium on the volume of the helix–coil transition of dA·dT polymers and their ligand complexes

The pressure dependence of the helix–coil transition of poly(dA)∙poly(dT) and poly[d(A-T)]·poly[d(A-T)] in aqueous solutions of NaCl and CsCl at concentrations between 10 and 200 mM is reported and used to calculate the accompanying volume change. We also investigated the binding parameters and volume change of ethidium bromide binding with poly(dA)∙poly(dT) and poly[d(A-T)]·poly[d(A-T)] in aqueous solutions of these two salts. The volume change of helix–coil transition of poly(dA)∙poly(dT) in Cs +-containing solutions differs by less than 1 cm 3 mol − 1 from the value measured when Na + is the counter-ion. We propose that this insensitivity towards salt type arises if the counter-ions are essentially fully hydrated around DNA and the DNA conformation is not significantly altered by salt types. Circular dichroism spectroscopy showed that the previously observed large volumetric disparity for the helix–coil transition of poly[d(A-T)]·poly[d(A-T)] in solutions containing Na + and Cs + is likely result of a Cs +-induced conformation change that is specific for poly[d(A-T)]·poly[d(A-T)]. This cation-specific conformation difference is mostly absent for poly(dA)∙poly(dT) and EB bound poly[d(A-T)]·poly[d(A-T)].

Melting and Swelling Behaviors of UV-Irradiated Gelatin Gel Microcapsules

Gelatin gel microcapsules with a narrow size distribution have been prepared for the use of regenerative therapy by means of SPG (Shirasu porous glass) emulsification and UV-induced cross linking, and the melting and swelling behaviors of the gel membrane of the microcapsules were observed. The gel melting temperature was proportional to the 2/3 power of UV irradiation time t for t<or=1 h and deviated from the 2/3 power behavior for t>or=1 h. The average cross-sectional area of the microcapsules that remains insoluble normalized by that at 25 degrees C monotonically increased with temperature for t<or=1 h. It then decreased, passed a minimum, and increased at high temperature for t>or=1 h. Repeated quenching of the gel microcapsules between two temperatures (25 and 40 degrees C) induced a reversible size change, which was attributed to the helix-coil transition of collagen molecules locally. From a theoretical consideration of gel particles, the observed gel melting behavior was explained well, and the scaled volume of the microcapsules was expressed as a function of scaled temperature with four fitting parameters for t<or=1 h.

The helix–coil transition revisited

In this article, we perform a dynamic Monte Carlo simulation study of the helix-coil transition by using a bond-fluctuation lattice model. The results of the simulations are compared with those predicted by the Zimm-Bragg statistical thermodynamic theory with propagation and nucleation parameters determined from simulation data. The Zimm-Bragg theory provides a satisfactory description of the helix-coil transition of a homopolypeptide chain of 32 residues (N = 32). For such a medium-length chain, however, the analytical equation based on a widely-used large-N approximation to the Zimm-Bragg theory is not suitable to predict the average length of helical blocks at low temperatures when helicity is high. We propose an analytical large-eigenvalue (lambda) approximation. The new equation yields a significantly improved agreement on the average helix-block length with the original Zimm-Bragg theory for both medium and long chain lengths in the entire temperature range. Nevertheless, even the original Zimm-Bragg theory does not provide an accurate description of helix-coil transition for longer chains. We assume that the single-residue nucleation of helix formation as suggested in the original Zimm-Bragg model might be responsible for this deviation. A mechanism of nucleation by a short helical block is proposed by us and provides a significantly improved agreement with our simulation data.

The structure factor and dynamics of the helix–coil transition

Thermodynamical properties of the helix–coil transition were successfully described in thepast by the model of Lifson, Poland and Sheraga. Here we compute the correspondingstructure factor and show that it possesses a universal scaling behaviour near the transitionpoint, even when the transition is of first order. Moreover, we introduce a dynamicalversion of this model, that we solve numerically. A Langevin equation is alsoproposed, to describe the dynamics of the density of hydrogen bonds. Analyticalsolution of this equation shows dynamical scaling near the critical temperature andpredicts a gelation phenomenon above the critical temperature. In the case whencomparison of the two dynamical approaches is possible, the predictions of ourphenomenological theory agree with the results of the Monte Carlo simulations.

On the helix-coil transition in alanine based polypeptides in gas phase

Using multicanonical simulations, the authors study the effect of charged end groups on helix formation in alanine based polypeptides. They confirm earlier reports that neutral polyalanine exhibits a pronounced helix-coil transition in gas phase simulations. Introducing a charged Lys+ at the C terminal stabilizes the alpha helix and leads to a higher transition temperature. On the other hand, adding the Lys+ at the N terminal inhibits helix formation. Instead, a more globular structure was found. These results are in agreement with recent experiments on alanine based polypeptides in gas phase. They indicate that present force fields describe accurately the intramolecular interactions in proteins.

Supersymmetric Langevin equation to explore free-energy landscapes

The recently discovered supersymmetric generalizations of the Langevin dynamics and Kramers equation can be utilized for the exploration of free-energy landscapes of systems whose large time-scale separation hampers the usefulness of standard molecular dynamics techniques. The first realistic application is here presented. The system chosen is a minimalist model for a short alanine peptide exhibiting a helix-coil transition.

Helix–Coil Transitions in Nonpolar Peptides

A Monte Carlo simulation of the folding and unfolding of a two-dimensional model polypeptide, which has α-helical motifs, in nonpolar side chains were carried out. The terms that approximate the effect of the hydrophobic interaction in a solvent are phenomenologically included. Only three states were considered for each unit: extended with hydrogen bonds, turns and coils. We investigated the nature of hydration in the assembly process of α-helical stretches. The conversion exhibited transitions between three states: random coils (C) at a high temperature, helix bundles (B) at a medium temperature, and α-helices (H) without lateral hydrophobic bonds at a low temperature. Small hydrophobic interactions result in only the H–C transition lacking the B state. On the other hand, as the hydrophobic effect strengthens, the B state appears at a medium temperature. The B–C and B–H transitions appear as an all-or-none-type transition and a gradually diffused type transition, respectively. This problem is related to protein folding. In the simulation performed in this study, we discuss the cold denaturation of proteins from the viewpoint of B–H transitions.

Stretching of Homopolymeric RNA Reveals Single-Stranded Helices and Base-Stacking

We have found strong supporting evidence for the helical structures of single-stranded nucleic acids by stretching individual molecules of polyadenylic acid [poly(A)] and polycytidylic acid [poly(C)]. Analyzing the force versus extension data using a two-state elastic model in which random-coil domains alternate with rigid helical domains allows one to extract the thermodynamic and structural properties. In addition, it also yields moderate to low cooperativity of the helix-coil transition for poly(A) and poly(C), respectively.

An α-Helical Burst in the src SH3 Folding Pathway

Src SH3 is a small all-beta-sheet protein composed of a single domain. We studied the folding behavior of src SH3 at various conditions by circular dichroism (CD), fluorescence, and X-ray solution scattering methods. On the src SH3 folding pathway, an alpha-helix-rich intermediate appeared not only at subzero temperatures but also above 0 degrees C. The fraction of alpha-helix in the kinetically observed intermediate is ca. 26% based on the kinetic CD experiment. X-ray solution scattering revealed that the intermediate was compact but not fully packed. The analysis of CD implies that the amplitude of the burst phase is proportional to the helical fraction calculated according to the helix-coil transition theory. This strongly suggests that the initial folding core is formed by the collapse of much less stably existing alpha-helices.

Helix-coil transition in DNA in the presence of a denaturating agent

A theory of the helix-coil transition in solutions containing a denaturing agent is proposed. It is shown that, if the transition is induced by an increase in the concentration of the denaturant, the range of the conformational transition narrows with a growing activity of the agent. In contrast, if the transition is induced by temperature variation, addition of a denaturant makes the transition broader, the more so for a higher activity of the agent. The results of the computation agree with published experimental data.

Side-Chain and Backbone Ordering in Homopolymers

In order to study the relation between backbone and side-chain ordering in proteins, we have performed multicanonical simulations of deka-peptide chains with various side groups. Glu(10), Gln(10), Asp(10), Asn(10), and Lys(10) were selected to cover a wide variety of possible interactions between the side chains of the monomers. All homopolymers undergo helix-coil transitions. We found that peptides with long side chains that are capable of hydrogen bonding, i.e., Glu(10), and Gln(10), exhibit a second transition at lower temperatures connected with side-chain ordering. This occurs in the gas phase as well as in solvent, although the character of the side-chain structure is different in each case. However, in polymers with short side chains capable of hydrogen bonding, i.e., Asp(10) and Asn(10), side-chain ordering takes place over a wide temperature range and exhibits no phase transition-like character. Moreover, non-backbone hydrogen bonds show enhanced formation and fluctuations already at the helix-coil transition temperature, indicating competition between side-chain and backbone hydrogen bond formation. Again, these results are qualitatively independent of the environment. Side-chain ordering in Lys(10), whose side groups are long and polar, also takes place over a wide temperature range and exhibits no phase transition-like character in both environments. Reasons for the observed chain length threshold and consequences from these results for protein folding are discussed.

Equilibrium unfolding of the poly(glutamic acid)20 helix

The equilibrium structural ensemble of a 20-residue polyglutamic acid peptide (E(20)) was studied with FRET, circular dichroism, and molecular dynamics (MD) simulations. A FRET donor, o-aminobenzamide, and acceptor, 3-nitrotyrosine, were introduced at the N- and C-termini, respectively. Circular dichroism, steady state FRET, and time-resolved FRET measurements were employed to characterize the fraction helix and end-to-end distance under different pH conditions: pH 4 (60% alpha-helix), pH 6 (0% alpha-helix), and pH 9 (0% alpha-helix). At pH 4, the end-to-end distance was measured at 24 A and determined to be considerably less than the 31 A predicted for an alpha-helix of the same length. At pH 6 and 9, the end-to-end distance was measured at > 31 and 39 A respectively, both which are determined to be considerably greater than the 27 A predicted for a freely jointed random coil of the same length. To better understand the physical forces underlying the unusual helix-coil transition in this peptide, three theoretical MD models of E(20) were constructed: (1) a pure alpha-helix, (2) an alpha-helix with equivalent attractive intramolecular contacts, and (3) a weak alpha-helix with termini-weighted intramolecular contacts ("sticky ends"). Using MD simulations, the bent helix structure calculated from Model 3 was found to be the closest in agreement with the experimental data.

Statistical Mechanics of Helix Bundles Using a Dynamic Programming Approach

Despite much study, biomolecule folding cooperativity is not well understood. There are quantitative models for helix-coil transitions and for coil-to-globule transitions, but no accurate models yet treat both chain collapse and secondary structure formation together. We develop here a dynamic programming approach to statistical mechanical partition functions of foldamer chain molecules. We call it the ascending levels model. We apply it to helix-coil and helix-bundle folding and cooperativity. For 14- to 50-mer Baldwin peptides, the model gives good predictions for the heat capacity and helicity versus temperature and urea. The model also gives good fits for the denaturation of Oas's three-helix bundle B domain of protein A (F13W*) and synthetic protein alpha3C by temperature and guanidine. The model predicts the conformational distributions. It shows that these proteins fold with transitions that are two-state, although the transitions in the Baldwin helices are nearly higher order. The model shows that the recently developed three-helix bundle polypeptoids of Lee et al. fold anti-cooperatively, with a predicted value of DeltaHvH/DeltaHcal = 0.72. The model also predicts that two-helix bundles are unstable in proteins but stable in peptoids. Our dynamic programming approach provides a general way to explore cooperativity in complex foldable polymers.

Europium ion as a probe for binding sites to carrageenans

Carrageenans, sulfated polysaccharides extracted from red algae, present a coil-helix transition and helix aggregation dependence on the type and concentration of counterions. In this study, we focus attention on a mixed valence counterion system: Eu 3+/Na + or K + with different gel-forming carrageenans: kappa, iota, and kappa-2. Results of stationary and time-dependent luminescence showed to be a suitable tool to probe ion binding to both the negatively charged sulfate group and the hydroxyl groups present in the biopolymer. For lower europium ion concentrations, a single longer decay emission lifetime was detected, which was attributed to the binding of europium ion to the carrageenan sulfate groups. An additional decay ascribed to europium binding to hydroxyl groups was observed above a threshold concentration, and this decay was dependent on the carrageenan charge density. Symmetry of the europium ion microenvironment was estimated by the ratio between the intensities of its emission bands, which has been shown to depend on the concentration of europium ions and on the specificity of the monovalent counterion bound to the carrageenan.

Effect of electrical field on polypeptide phase behavior involving a conformationally coupled anisotropic–isotropic transition

Effect of external electrical field on phase equilibrium was reported for poly(γ-benzyl l-glutamate) (PBLG) in a mixed solvent containing denaturant acid where a helix–coil transition coupled anisotropic–isotropic transition exists. The experimental results revealed that the anisotropic phase and helix conformation can be stabilized when an external electrical field is applied. In the presence of electrical field, the anisotropic–isotropic phase boundary shifts to lower polymer concentrations and the helix–coil induced anisotropic–isotropic transition becomes stable in the denaturant acid. The lattice model derived in our previous work was further generalized by implementing a free energy term contributed from external orientational field of dipole type. The calculated phase diagrams have been compared with those experimentally observed. A good qualitative agreement has been achieved.

Short-time dynamics of polypeptides

The authors study the short-time dynamics of helix-forming polypeptide chains using an all-atom representation of the molecules and an implicit solvation model to approximate the interaction with the surrounding solvent. The results confirm earlier observations that the helix-coil transition in proteins can be described by a set of critical exponents. The high statistics of the simulations allows the authors to determine the exponent values with increased precision and support universality of the helix-coil transition in homopolymers and (helical) proteins.

How does the coupling of secondary and tertiary interactions control the folding of helical macromolecules?

The authors study how the simultaneous presence of short-range secondary and long-range tertiary interactions controls the folding and collapse behavior of a helical macromolecule. The secondary interactions stabilize the helical conformation of the chain, while the tertiary interactions govern its overall three-dimensional shape. The authors have carried out Monte Carlo simulations to study the effect of chain length on the folding and collapse behavior of the chain. They have calculated state diagrams for four chain lengths and found that the physics is very rich with a plethora of stable conformational states. In addition to the helix-coil and coil-globule transitions, their model describes the coupling between them which takes place at low temperatures. Under these conditions, their model predicts a cascade of continuous, conformational transitions between states with an increase in the strength of the tertiary interactions. During each transition the chain shrinks, i.e., collapses, in a rapid and specific manner. In addition, the number of the transitions increases with increasing chain length. They have also found that the low-temperature regions of the state diagram between the transition lines cannot be associated with specific structures of the chain, but rather, with ensembles of various configurations of the chain with similar characteristics. Based on these results the authors propose a mechanism for the folding and collapse of helical macromolecules which is further supported by the analysis of configurational, configurational, and thermodynamic properties of the chain.