Hydrogen bonds in polymer folding

α-Helix-Mediated Protein Adhesion

Proteins have been adopted by natural living organisms to create robust bioadhesive materials, such as biofilms and amyloid plaques formed in microbes and barnacles. In these cases, β-sheet stacking is recognized as a key feature that is closely related to the interfacial adhesion of proteins. Herein, we challenge this well-known recognition by proposing an α-helix-mediated interfacial adhesion model for proteins. By using bovine serum albumin (BSA) as a model protein, it was discovered that the reduction of disulfide bonds in BSA results in random coils from unfolded BSA dragging α-helices to gather at the solid/liquid interface (SLI). The hydrophobic residues in the α-helix then expose and break through the hydration layer of the SLI, followed by the random deposition of hydrophilic and hydrophobic residues to achieve interfacial adhesion. As a result, the first assembled layer is enriched in the α-helix secondary structure, which is then strengthened by intermolecular disulfide bonds and further initiates stepwise layering protein assembly. In this process, β-sheet stacking is transformed from the α-helix in a gradually evolving manner. This finding thus indicates a valuable clue that β-sheet-featuring amyloid may form after the interfacial adhesion of proteins. Furthermore, the finding of the α-helix-mediated interfacial adhesion model of proteins affords a unique strategy to prepare protein nanofilms with a well-defined layer number, presenting robust and modulable adhesion on various substrates and exhibiting good resistance to acid, alkali, organic solvent, ultrasonic, and adhesive tape peeling.

Switchable helical structures formed by the hierarchical self-assembly of laterally tethered nanorods

The formation of helical scrolls formed by self-assembly of tethered nanorod amphiphiles and their molecular analogs are investigated. A model bilayer sheet assembled by laterally tethered nanorods is simulated and shown that it can fold into distinct helical morphologies under different solvent conditions. The helices can reversibly transform from one morphology to another by dynamically changing the solvent condition. This model serves both to inspire the fabrication of laterally tethered nanorods for assembling helices at nanometer scales and as a proof-of-concept for engineering switchable nanomaterials via hierarchical self-assembly.

A theoretical study of red-shifting and blue-shifting hydrogen bonds occurring between imidazolidine derivatives and PEG/PVP polymers

A theoretical study is presented with the aim to investigate the molecular properties of intermolecular complexes formed by the monomeric units of polyvinylpyrrolidone (PVP) or polyethyleneglycol (PEG) polymers and a set of four imidazolidine (hydantoine) derivatives. The substitution of the carbonyl groups for thiocarbonyl in the hydantoin scaffold was taken into account when analyzing the effect of the hydrogen bonds on imidazolidine derivatives. B3LYP/6-31G(d,p) calculations and topological integrations derived from the quantum theory of atoms in molecules (QTAIM) were applied with the purpose of examining the N-H···O hydrogen bond strengths formed between the amide group of the hydantoine ring and the oxygen atoms of PVP and PEG polymers. The effects caused by the N-H···O interaction fit the typical evidence for hydrogen bonds, which includes a variation in the stretch frequencies of the N-H bonds. These frequencies were identified as being vibrational red-shifts because their values decreased. Although the values of such calculated interaction energies are between 12 and 33 kJ mol(-1), secondary intermolecular interactions were also identified. One of these secondary interactions is formed through the interaction of the benzyl hydrogen atoms with the oxygen atoms of the PVP and PEG structures. As such, we have analyzed the stretch frequencies on the C-H bonds of the benzyl groups, and blue-shifts were identified on these bonds. In this sense, the intermolecular systems formed by hydantoine derivatives and PVP/PEG monomers were characterized as a mix of red-shifting and blue-shifting hydrogen-bonded complexes.

Alternative hydrogen bond implementations produce opposite effects on collapse cooperativity of lattice homopolypeptide models

We use complete enumeration of self-avoiding chains of up to N=26 monomers in two-dimensional lattices to investigate the effect of alternative implementations of backbone hydrogen bonds on the cooperativity of homopolypeptide collapse. Following a recent study on protein folding models, we use the square lattice with z=3 local conformations per monomer and lattice extensions containing diagonal steps which result in z=5 or z=7 and assume that only a subset of zh<z local conformations is compatible with hydrogen bond formation. As previously observed in heteropolymeric folding, a significant increase in cooperativity, as measured by kappa2 values, results from the coupling between hydrogen bonds and hydrophobic interactions, in such a way that hydrophobic contacts are favorable only when contacting monomers are involved in hydrogen bond formation. For some z/zh combinations the energy distribution is bimodal at the collapse transition temperature. The situation can be regarded as if all hydrophobic contacts actually decrease the energy by the same amount, 2h , with the addition of an energetic increase, epsilon2=h, as a penalty for each contacting monomer not satisfying the hydrogen bond condition. Cooperativity is little affected and might even decrease, however, when hydrogen bonds produce a decrease in energy by the same amount, epsilon1=h, for each bonding monomer. For the more general situation when the hydrogen bond effect is not equal, in modulus, to the hydrophobic interaction, i.e., epsilon2 not equalh or epsilon1 not equal h, we observe a pronounced increase in kappa2 for small epsilon2, with a maximum around epsilon2/h approximately 1.5, followed by a gradual decrease to a limiting value at large epsilon2. The opposite behavior is observed when epsilon1 is varied. The observed qualitative difference is shown to arise from opposite effects on the convexity of the total density of states of the system when subdensities corresponding to different numbers of hydrogen bonds are differently favored as opposed to the case when subdensities corresponding to different numbers of contacting monomers not forming hydrogen bonds are differently unfavored. Potential implications for the cooperativity of protein folding and protein unspecific collapse are discussed.

Topology of pseudoknotted homopolymers

We consider the folding of a self-avoiding homopolymer on a lattice, with saturating hydrogen bond interactions. Our goal is to numerically evaluate the statistical distribution of the topological genus of pseudoknotted configurations. The genus has been recently proposed for classifying pseudoknots (and their topological complexity) in the context of RNA folding. We compare our results on the distribution of the genus of pseudoknots, with the theoretical predictions of an existing combinatorial model for an infinitely flexible and stretchable homopolymer. We thus obtain that steric and geometric constraints considerably limit the topological complexity of pseudoknotted configurations, as it occurs for instance in real RNA molecules. We also analyze the scaling properties at large homopolymer length, and the genus distributions above and below the critical temperature between the swollen phase and the compact-globule phase, both in two and three dimensions.

Entropy reduction effect imposed by hydrogen bond formation on protein folding cooperativity: evidence from a hydrophobic minimalist model

Conformational restrictions imposed by hydrogen bond formation during protein folding are investigated by Monte Carlo simulations of a non-native-centric, two-dimensional, hydrophobic model in which the formation of favorable contacts is coupled to an effective reduction in lattice coordination. This scheme is intended to mimic the requirement that polar backbone groups of real proteins must form hydrogen bonds concomitantly to their burial inside the apolar protein core. In addition to the square lattice, with z=3 conformations per monomer, we use extensions in which diagonal step vectors are allowed, resulting in z=5 and z=7. Thermodynamics are governed by the hydrophobic energy function, according to which hydrophobic monomers tend to make contacts unspecifically while the reverse is true for hydrophilic monomers, with the additional restriction that only contacts between monomers adopting one of zh<z local conformations contribute to the energy, where zh is the number of local conformations assumed to be compatible with hydrogen bond formation. The folding transition abruptness and van't Hoff-to-calorimetric-enthalpy ratio are found to increase dramatically by this simple and physically motivated mechanism. The observed increase in folding cooperativity is correlated to an increase in the convexity of the underlying microcanonical conformational entropy as a function of energy. Preliminary simulations in three dimensions, even though using a smaller relative reduction in lattice effective coordination zh/z=4/5, display a slight increase in cooperativity for a hydrophobic model of 40 monomers and a more pronounced increase in cooperativity for a native-centric Go-model with the same native conformation, suggesting that this purely entropic effect is not an artifact of dimensionality and is likely to be of fundamental importance in the theoretical understanding of folding cooperativity.

Compact phases of polymers with hydrogen bonding

We propose an off-lattice model for a self-avoiding homopolymer chain with two different competing attractive interactions, mimicking the hydrophobic effect and the hydrogen-bond formation, respectively. By means of Monte Carlo simulations, we are able to trace out the complete phase diagram for different values of the relative strengths of the two competing interactions. For strong enough hydrogen bonding, the ground state is a helical conformation, whereas with decreasing hydrogen-bonding strength, helices get eventually destabilized at low temperature in favor of more compact conformations resembling beta sheets appearing in the native structures of proteins. For weaker hydrogen bonding helices are not thermodynamically relevant anymore.

Structural and folding properties of a lattice prion model

Searching through and conducting Monte Carlo folding simulations on 10(6) different 27 mer sequences, we have selected a prionlike lattice model whose energy spectrum and folding properties demonstrate characteristic prion behavior. The energetic competition and structural partition between two closely spaced energy minima yield unique kinetic and thermodynamic properties that can be qualitatively compared with experimental results. Folding simulations indicate that the probability of reaching the first excited state from a denatured random conformation is much higher than the probability of reaching the global energy-minimum state.

Importance of secondary structural specificity determinants in protein folding: insertion of a native beta-sheet sequence into an alpha-helical coiled-coil

To examine how a short secondary structural element derived from a native protein folds when in a different protein environment, we inserted an 11-residue beta-sheet segment (cassette) from human immunoglobulin fold, Fab new, into an alpha-helical coiled-coil host protein (cassette holder). This de novo design protein model, the structural cassette mutagenesis (SCM) model, allows us to study protein folding principles involving both short- and long-range interactions that affect secondary structure stability and conformation. In this study, we address whether the insertion of this beta-sheet cassette into the alpha-helical coiled-coil protein would result in conformational change nucleated by the long-range tertiary stabilization of the coiled-coil, therefore overriding the local propensity of the cassette to form beta-sheet, observed in its native immunoglobulin fold. The results showed that not only did the nucleating helices of the coiled-coil on either end of the cassette fail to nucleate the beta-sheet cassette to fold with an alpha-helical conformation, but also the entire chimeric protein became a random coil. We identified two determinants in this cassette that prevented coiled-coil formation: (1) a tandem dipeptide NN motif at the N-terminal of the beta-sheet cassette, and (2) the hydrophilic Ser residue, which would be buried in the hydrophobic core if the coiled-coil structure were to fold. By amino acid substitution of these helix disruptive residues, that is, either the replacement of the NN motif with high helical propensity Ala residues or the substitution of Ser with Leu to enhance hydrophobicity, we were able to convert the random coil chimeric protein into a fully folded alpha-helical coiled-coil. We hypothesized that this NN motif is a "secondary structural specificity determinant" which is very selective for one type of secondary structure and may prevent neighboring residues from adopting an alternate protein fold. These sequences with secondary structural specificity determinants have very strong local propensity to fold into a specific secondary structure and may affect overall protein folding by acting as a folding initiation site.