Role of electrostatic screening in determining protein main chain conformational preferences

Influence of ion specificity and concentration on the conformational transition of intrinsically disordered sheep prion peptide

The structural sensitivity of the IDPs with the ions has been observed experimentally; however, it is still unclear how the presence of different metal ions affects structural stability. We performed atomistic molecular dynamics simulation of sheep prion peptide (142-167) in presence of different monovalent, divalent ions at various concentrations to find out the effect of the size, charge, and ionic concentration on the structure of the peptide. It is found that Li + ions have a higher survival probability compared to Na + , K + and Mg2 + affecting the solvation structure of the protein leading to the alpha-helix structure. At high concentration, due to the increase in the ion-solvent and ion-counter interactions, the effect of the ions is screened on the surface of the protein and hence no ion specificity is observed. This study demonstrates how ions can be used to regulate the protein structure and function that can help in designing drugs.

Normal mode calculation and infrared spectroscopy of proteins in water solution: Relationship between amide I transition dipole strength and secondary structure

Dipole Strength (DS) of the amides has gained a renewed interest in chemical physics since it provides an important tool to disclose the on-site vibrational energy distributions. Apart from earlier experimental efforts on polypeptides, little is still known about DS in complex proteins. We accurately measured the Fourier Transform Infrared absorption spectra of nine proteins in water solution obtaining their Molar Extinction Coefficient in the amide I and II spectral region. Our results show that the amide I DS value depends on the protein secondary structure, being that of the α-rich and unstructured proteins lower by a factor of 2 than that of the β-rich proteins. The average DS for amino acids in α and β secondary structures confirms this finding. Normal Mode calculation and Molecular Dynamics were performed and used as tools for data analysis and interpretation. The present outcomes corroborate the hypothesis that antiparallel β-sheet environment is more prone to delocalize the on-site CO stretching vibration through coupling mechanisms between carbonyl groups, whereas α-helix structures are energetically less stable to permit vibrational mode delocalization.

Implicit water model within the Zimm-Bragg approach to analyze experimental data for heat and cold denaturation of proteins

Studies of biopolymer conformations essentially rely on theoretical models that are routinely used to process and analyze experimental data. While modern experiments allow study of single molecules in vivo, corresponding theories date back to the early 1950s and require an essential update to include the recent significant progress in the description of water. The Hamiltonian formulation of the Zimm-Bragg model we propose includes a simplified, yet explicit model of water-polypeptide interactions that transforms into the equivalent implicit description after performing the summation of solvent degrees of freedom in the partition function. Here we show that our model fits very well to the circular dichroism experimental data for both heat and cold denaturation and provides the energies of inter- and intra-molecular H-bonds, unavailable with other processing methods. The revealed delicate balance between these energies determines the conditions for the existence of cold denaturation and thus clarifies its absence in some proteins.

Cytotoxic species in amyloid-associated diseases: Oligomers or mature fibrils

Amyloid diseases especially, Alzheimer's disease (AD), is characterized by an imbalance between the production and clearance of amyloid-β (Aβ) species. Amyloidogenic proteins or peptides can transform structurally from monomers into β-stranded fibrils via multiple oligomeric states. Among various amyloid species, structured oligomers are proposed to be more toxic than fibrils; however, the identification of amyloid oligomers has been challenging due to their heterogeneous and metastable nature. Multiple techniques have recently helped in better understanding of oligomer's assembly details and structural properties. Moreover, some progress on elucidating the mechanisms of oligomer-triggered toxicity has been made. Based on the collection of current findings, there is growing consensus that control of toxic amyloid oligomers could be a valid approach to regulate amyloid-associated toxicity, which could advance development of new diagnostics and therapeutics for amyloid-related diseases. In this review, we have described the recent scenario of amyloid diseases with a great deal of information about the recent understanding of oligomers' assembly, structural properties, and toxicity. Also comprehensive details have been provided to differentiate the degree of toxicity associated with prefibrillar aggregates.

The effects of solution additives and gas-phase modifiers on the molecular environment and conformational space of common heme proteins

RATIONALE

The molecular environment is known to impact the secondary and tertiary structures of biomolecules both in solution and in the gas phase, shifting the equilibrium between different conformational and oligomerization states. However, there is a lack of studies monitoring the impacts of solution additives and gas-phase modifiers on biomolecules characterized using ion mobility techniques.

METHODS

The effect of solution additives and gas-phase modifiers on the molecular environment of two common heme proteins, bovine cytochrome c and equine myoglobin, is investigated as a function of the time after desolvation (e.g., 100-500 ms) using nanoelectrospray ionization coupled to trapped ion mobility spectrometry with detection by time-of-flight mass spectrometry. Organic compounds used as additives/modifiers (methanol, acetonitrile, acetone) were either added to the aqueous protein solution before ionization or added to the ion mobility bath gas by nebulization.

RESULTS

Changes in the mobility profiles are observed depending on the starting solution composition (i.e., in aqueous solution at neutral pH or in the presence of organic content: methanol, acetone, or acetonitrile) and the protein. In the presence of gas-phase modifiers (i.e., N₂ doped with methanol, acetone, or acetonitrile), a shift in the mobility profiles driven by the gas-modifier mass and size and changes in the relative abundances and number of IMS bands are observed.

CONCLUSIONS

We attribute the observed changes in the mobility profiles in the presence of gas-phase modifiers to a clustering/declustering mechanism by which organic molecules adsorb to the protein ion surface and lower energetic barriers for interconversion between conformational states, thus redefining the free energy landscape and equilibria between conformers. These structural biology experiments open new avenues for manipulation and interrogation of biomolecules in the gas phase with the potential to emulate a large suite of solution conditions, ultimately including conditions that more accurately reflect a variety of intracellular environments.

A component analysis of the free energies of folding of 35 proteins: A consensus view on the thermodynamics of folding at the molecular level

What factors favor protein folding? This is a textbook question. Parsing the experimental free energies of folding/unfolding into diverse enthalpic and entropic components of solute and solvent favoring or disfavoring folding is not an easy task. In this study, we present a computational protocol for estimating the free energy contributors to protein folding semi-quantitatively using ensembles of unfolded and native states generated via molecular dynamics simulations. We tested the methodology on 35 proteins with diverse structural motifs and sizes and found that the calculated free energies correlate well with experiment (correlation coefficient ∼ 0.85), enabling us to develop a consensus view of the energetics of folding. As a more sensitive test of the methodology, we also investigated the free energies of folding of an additional 33 single point mutants and obtained a correlation coefficient of 0.8. A notable observation is that the folding free energy components appear to carry signatures of the fold (SCOP classification) of the protein. © 2017 Wiley Periodicals, Inc.

Shielding effect in protein folding

One of the most important interactions responsible for protein folding and stability are hydrogen bonds between peptide groups. There is a constant competition between the water molecules and peptide groups in a hydrogen bond formation. Also side-chains take part in this process by reducing hydration of peptide group (shielding effect) that promotes the protein folding. In this paper, a new approach to take into account a shielding effect is presented. A modification of the energy function is derived and incorporated into the UNited RESidue (UNRES) force field. Canonical Molecular Dynamics and Replica Exchange Molecular Dynamics with UNRES force field is applied to study the influence of this effect on protein structure, folding kinetics and free energy landscapes. The results of test calculations suggest that even small contribution of this effect into energy function changes force field behavior as well as speeds up the folding process significantly.

Scrutiny of electrostatic-driven conformational ordering of polypeptide chains in DMSO: a study with a model oligopeptide

The molecular mechanism of DMSO-induced stabilisation of β-sheets is attributed to the combination of polar electrostatic interactions among side chains, and backbone desolvation through bulky side chains which promotes backbone hydrogen bonding.

Origin of hydrophobicity and enhanced water hydrogen bond strength near purely hydrophobic solutes

Hydrophobicity plays an important role in numerous physicochemical processes from the process of dissolution in water to protein folding, but its origin at the fundamental level is still unclear. The classical view of hydrophobic hydration is that, in the presence of a hydrophobic solute, water forms transient microscopic "icebergs" arising from strengthened water hydrogen bonding, but there is no experimental evidence for enhanced hydrogen bonding and/or icebergs in such solutions. Here, we have used the redshifts and line shapes of the isotopically decoupled IR oxygen-deuterium (O-D) stretching mode of HDO water near small purely hydrophobic solutes (methane, ethane, krypton, and xenon) to study hydrophobicity at the most fundamental level. We present unequivocal and model-free experimental proof for the presence of strengthened water hydrogen bonds near four hydrophobic solutes, matching those in ice and clathrates. The water molecules involved in the enhanced hydrogen bonds display extensive structural ordering resembling that in clathrates. The number of ice-like hydrogen bonds is 10-15 per methane molecule. Ab initio molecular dynamics simulations have confirmed that water molecules in the vicinity of methane form stronger, more numerous, and more tetrahedrally oriented hydrogen bonds than those in bulk water and that their mobility is restricted. We show the absence of intercalating water molecules that cause the electrostatic screening (shielding) of hydrogen bonds in bulk water as the critical element for the enhanced hydrogen bonding around a hydrophobic solute. Our results confirm the classical view of hydrophobic hydration.

Introducing folding stability into the score function for computational design of RNA-binding peptides boosts the probability of success

A computational strategy that integrates our peptide search algorithm with atomistic molecular dynamics simulation was used to design rational peptide drugs that recognize and bind to the anticodon stem and loop domain (ASL(Lys3)) of human tRNAUUULys3 for the purpose of interrupting HIV replication. The score function of the search algorithm was improved by adding a peptide stability term weighted by an adjustable factor λ to the peptide binding free energy. The five best peptide sequences associated with five different values of λ were determined using the search algorithm and then input in atomistic simulations to examine the stability of the peptides' folded conformations and their ability to bind to ASL(Lys3). Simulation results demonstrated that setting an intermediate value of λ achieves a good balance between optimizing the peptide's binding ability and stabilizing its folded conformation during the sequence evolution process, and hence leads to optimal binding to the target ASL(Lys3). Thus, addition of a peptide stability term significantly improves the success rate for our peptide design search.

Probing the role of electrostatics of polypeptide main-chain in protein folding by perturbing N-terminal residue stereochemistry: DFT study with oligoalanine models

Energetics of folding (ΔH_E→F, in kcal mol⁻¹) from the extended (E) structure to the folded (F) structure for Ia and Ib critically depend on the geometrical relationship between the backbone peptide units of the polypeptide structure.

Trapping and Driving Individual Charged Micro-particles in Fluid with an Electrostatic Device

A variety of micro-tweezers techniques, such as optical tweezers, magnetic tweezers, and dielectrophoresis technique, have been applied intensively in precise characterization of micro/nanoparticles and bio-molecules. They have contributed remarkably in better understanding of working mechanisms of individual sub-cell organelles, proteins, and DNA. In this paper, we present a controllable electrostatic device embedded in a microchannel, which is capable of driving, trapping, and releasing charged micro-particles suspended in microfluid, demonstrating the basic concepts of electrostatic tweezers. Such a device is scalable to smaller size and offers an alternative to currently used micro-tweezers for application in sorting, selecting, manipulating, and analyzing individual micro/nanoparticles. Furthermore, the system offers the potential in being combined with dielectrophoresis and other techniques to create hybrid micro-manipulation systems.

Algorithm to design inhibitors using stereochemically mixed l,d polypeptides: Validation against HIV protease

Polypeptides have potential to be designed as drugs or inhibitors against the desired targets. In polypeptides, every chiral α-amino acid has enantiomeric structural possibility to become l or d amino acids and can be used as design monomer. Among the various possibilities, use of stereochemistry as a design tool has potential to determine both functional specificity and metabolic stability of the designed polypeptides. The polypeptides with mixed l,d amino acids are a class of peptidomimitics, an attractive drug like molecules and also less susceptible to proteolytic activities. Therefore in this study, a three step algorithm is proposed to design the polypeptides against desired drug targets. For this, all possible configurational isomers of mixed l,d polyleucine (Ac-Leu8-NHMe) structure were randomly modeled with simulated annealing molecular dynamics and the resultant library of discrete folds were scored against HIV protease as a model target. The best scored folds of mixed l,d structures were inverse optimized for sequences in situ and the resultant sequences as inhibitors were validated for conformational integrity using molecular dynamics. This study presents and validates an algorithm to design polypeptides of mixed l,d structures as drugs/inhibitors by inverse fitting them as molecular ligands against desired target.

Mechanism of stabilization of helix secondary structure by constrained Cα-tetrasubstituted α-amino acids

The theoretical basis behind the ability of constrained Cα-tetrasubstituted amino acids (CTAAs) to induce stable helical conformations has been studied through Replica Exchange Molecular Dynamics Potential of Mean Force Quantum Theory of Atoms In Molecules calculations on Ac-l-Ala-CTAA-l-Ala-Aib-l-Ala-NHMe peptide models. We found that the origin of helix stabilization by CTAAs can be ascribed to at least two complementary mechanisms limiting the backbone conformational freedom: steric hindrance predominantly in the (+x,+y,-z) sector of a right-handed 3D Cartesian space, where the z axis coincides with the helical axis and the Cα of the CTAA lies on the +y axis (0,+y,0), and the establishment of additional and relatively strong C-H···O interactions involving the CTAA.

Molecular recognition mechanism of peptide chain bound to the tRNA(Lys3) anticodon loop in silico

The mechanism by which proteins recognize and bind the post-transcriptional modifications of RNAs is unknown, yet these interactions play important functions in biology. Atomistic molecular dynamics simulations were performed to examine the folding of the model peptide chain -RVTHHAFLGAHRTVG- and the complex formed by the folded peptide with the native anticodon stem and loop of the human tRNA(Lys3) (hASL(Lys3)) in order to explore the binding mechanism. By analyzing and comparing two folded conformations of this peptide obtained from the folding simulation, we found that the van der Waals (VDW) energy is necessary for the thermal stability of the peptide, and the charge-charge (ELE + EGB) energy is crucial for determining the three-dimensional folded structure of the peptide backbone. Subsequently, two conformations of the peptide were employed to investigate their binding behaviors to hASL(Lys3). The metastable folded peptide was found to bind to hASL(Lys3) much easier than the stable folded peptide in the binding simulations. An energetic analysis reveals that the VDW energy favors the binding, whereas the ELE + EGB energies disfavor the binding. Arginines on the peptide preferentially attract the phosphate backbone via the inter-chain ELE + EGB interaction, significantly contributing to the binding affinity. The hydrophobic phenylalanine interacts with the anticodon loop of hASL(Lys3) via the inter-chain VDW interaction, significantly contributing to the binding specificity.

De novo design of stable α-helices

Recent studies have elucidated key principles governing folding and stability of α-helices in short peptides and globular proteins. In this chapter we review briefly those principles and describe a protocol for the de novo design of highly stable α-helixes using the SEQOPT algorithm. This algorithm is based on AGADIR, the statistical mechanical theory for helix-coil transitions in monomeric peptides, and the tunneling algorithm for global sequence optimization.

Computational and theoretical methods for protein folding

A computational approach is essential whenever the complexity of the process under study is such that direct theoretical or experimental approaches are not viable. This is the case for protein folding, for which a significant amount of data are being collected. This paper reports on the essential role of in silico methods and the unprecedented interplay of computational and theoretical approaches, which is a defining point of the interdisciplinary investigations of the protein folding process. Besides giving an overview of the available computational methods and tools, we argue that computation plays not merely an ancillary role but has a more constructive function in that computational work may precede theory and experiments. More precisely, computation can provide the primary conceptual clues to inspire subsequent theoretical and experimental work even in a case where no preexisting evidence or theoretical frameworks are available. This is cogently manifested in the application of machine learning methods to come to grips with the folding dynamics. These close relationships suggested complementing the review of computational methods within the appropriate theoretical context to provide a self-contained outlook of the basic concepts that have converged into a unified description of folding and have grown in a synergic relationship with their computational counterpart. Finally, the advantages and limitations of current computational methodologies are discussed to show how the smart analysis of large amounts of data and the development of more effective algorithms can improve our understanding of protein folding.

Mechanisms of amyloid fibril formation--focus on domain-swapping

Conformational diseases constitute a group of heterologous disorders in which a constituent host protein undergoes changes in conformation, leading to aggregation and deposition. To understand the molecular mechanisms of the process of amyloid fibril formation, numerous in vitro and in vivo studies, including model and pathologically relevant proteins, have been performed. Understanding the molecular details of these processes is of major importance to understand neurodegenerative diseases and could contribute to more effective therapies. Many models have been proposed to describe the mechanism by which proteins undergo ordered aggregation into amyloid fibrils. We classify these as: (a) templating and nucleation; (b) linear, colloid-like assembly of spherical oligomers; and (c) domain-swapping. In this review, we stress the role of domain-swapping and discuss the role of proline switches.

Creating novel protein scripts beyond natural alphabets

Natural proteins are concatenated amino acids with definite handedness or chirality, with their spatial orientation being preferentially left handed or L-chiral. This paper discusses the biophysics of stereo-chemical perturbation to proteins using D-(α) amino acid and its utility as an additional design alphabet while scripting novel protein structures.

Protein homomers in point-group assembly: symmetry making and breaking are specific and distinctive in their codes of chemical alphabet in side chains

Oligomerizing to point-group symmetry, protein oligomers need to have the symmetry broken for biologically crucial functions, such as, allosteric regulation, enzyme catalysis, and so forth. In the making of symmetry, based on self assembly, and the breaking of symmetry, based on intermolecular interactions, proteins may manifest, like their other functions, specific scripts over the coding alphabet in side chains. To address the possibility, we analyzed 82 protein homodimers in their C(2)-symmetry-related side chains across noncrystallographic interfaces, to know if they may be identical or distinct in conformation, and thus conserved or broken in symmetry. We find the propensity to conformational mismatch across interfaces correlated with side-chain chemical structure, low to very low in aromatic Trp, Tyr, His, Phe, and Arg, and high to very high in aliphatic Val, Pro, Met, Glu, Ser, Lys, Gln, Asn, and Asp, related not to polarity but, interestingly, to aromaticity of the structure. The organizational plan having aromatics embedded in a hub of aliphatic-nonpolar groups and a surrounding rim of aliphatic-polar groups, called "hotspot," has been known to direct protein-protein interaction. Finding conformational-mismatch propensities of side chains congruous with their specific chemical roles in protein-protein interaction, we propose that aromatic side chains will drive protein homomers to high symmetry, while polar- and nonpolar aliphatic side chains will drive them to the functionally-necessitated breaks of symmetry. Side chains are in their roles as protein-coding alphabet illuminated in the physics, which is discussed.

Position-specific propensities of amino acids in the β-strand

Background

Despite the importance of β-strands as main building blocks in proteins, the propensity of amino acid in β-strands is not well-understood as it has been more difficult to determine experimentally compared to α-helices. Recent studies have shown that most of the amino acids have significantly high or low propensity towards both ends of β-strands. However, a comprehensive analysis of the sequence dependent amino acid propensities at positions between the ends of the β-strand has not been investigated.

Results

The propensities of the amino acids calculated from a large non-redundant database of proteins are found to be highly position-specific and vary continuously throughout the length of the β-strand. They follow an unexpected characteristic periodic pattern in inner positions with respect to the cap residues in both termini of β-strands; this periodic nature is markedly different from that of the α-helices with respect to the strength and pattern in periodicity. This periodicity is not only different for different amino acids but it also varies considerably for the amino acids belonging to the same physico-chemical group. Average hydrophobicity is also found to be periodic with respect to the positions from both termini of β-strands.

Conclusions

The results contradict the earlier perception of isotropic nature of amino acid propensities in the middle region of β-strands. These position-specific propensities should be of immense help in understanding the factors responsible for β-strand design and efficient prediction of β-strand structure in unknown proteins.

A free-energy approach for all-atom protein simulation

All-atom free-energy methods offer a promising alternative to kinetic molecular mechanics simulations of protein folding and association. Here we report an accurate, transferable all-atom biophysical force field (PFF02) that stabilizes the native conformation of a wide range of proteins as the global optimum of the free-energy landscape. For 32 proteins of the ROSETTA decoy set and six proteins that we have previously folded with PFF01, we find near-native conformations with an average backbone RMSD of 2.14 A to the native conformation and an average Z-score of -3.46 to the corresponding decoy set. We used nonequilibrium sampling techniques starting from completely extended conformations to exhaustively sample the energy surface of three nonhomologous hairpin-peptides, a three-stranded beta-sheet, the all-helical 40 amino-acid HIV accessory protein, and a zinc-finger beta beta alpha motif, and find near-native conformations for the minimal energy for each protein. Using a massively parallel evolutionary algorithm, we also obtain a near-native low-energy conformation for the 54 amino-acid engrailed homeodomain. Our force field thus stabilized near-native conformations for a total of 20 proteins of all structure classes with an average RMSD of only 3.06 A to their respective experimental conformations.

Modeling of peptides containing D-amino acids: implications on cyclization

Cyclic peptides are therapeutically attractive due to their high bioavailability, potential selectivity, and scaffold novelty. Furthermore, the presence of D-residues induces conformational preferences not followed by peptides consisting of naturally abundant L-residues. Therefore, comprehending how amino acids induce turns in peptides, subsequently facilitating cyclization, is significant in peptide design. Here, we performed 20-ns explicit-solvent molecular dynamics simulations for three diastereomeric peptides with stereochemistries: LLLLL, LLLDL, and LDLDL. Experimentally LLLLL and LDLDL readily cyclize, whereas LLLDL cyclizes in low yield. Simulations at 310 K produced conformations with inter-terminal hydrogen bonds that correlated qualitatively with the experimental cyclization trend. Energies obtained for representative structures from quantum chemical (B3LYP/PCM/cc-pVTZ//HF/6-31G*) calculations predicted pseudo-cyclic and extended conformations as the most stable for LLLLL and LLLDL, respectively, in agreement with the experimental data. In contrast, the most stable conformer predicted for peptide LDLDL was not a pseudo-cyclic structure. Moreover, D-residues preferred the experimentally less populated alpha(L) rotamers even when simulations were performed at a higher temperature and with strategically selected starting conformations. Energies calculated with molecular mechanics were consistent only with peptide LLLLL. Thus, the conformational preferences obtained for the all L: -amino acid peptide were in agreement with the experimental observations. Moreover, refinement of the force field is expected to provide far-reaching conformational sampling of peptides containing D-residues to further develop force field-based conformational-searching methods.

Origin of the change in solvation enthalpy of the peptide group when neighboring peptide groups are added

Recent calorimetric measurements of the solvation enthalpies of some dipeptide analogs confirm our earlier prediction that the principle of group additivity is not valid for the interaction of the peptide group with water. We examine the consequences for understanding the properties of peptide solvation. A major consequence is that the current value of the peptide-solvation enthalpy, which is a basic parameter in analyzing the energetics of protein folding, is seriously wrong. Electrostatic calculations of solvation-free energies provide an estimate of the size and nature of the error. Peptide hydrogen exchange rates provide an experimental approach for testing the accuracy of the solvation-free energies of peptide groups found by electrostatic calculations. These calculations emphasize that ignoring electrostatic interactions with neighboring NHCO groups should be a major source of error. Results in 1972 for peptide hydrogen exchange rates demonstrate that peptide-solvation-free energies are strongly affected by adjoining NHCO groups. In the past, the effect of adjoining peptide groups on the exchange rate of a peptide NH proton was treated as an inductive effect. The effect can be calculated, however, by an electrostatic model with fixed partial charges and a continuum solvent.

Protein design with L- and D-alpha-amino acid structures as the alphabet

Summarizing the implications of homochiral structures in interpeptide interactions, not only in the topology but also possibly in the physics of protein folding, this Account provides an overview of the concept of shape-specific protein design using D- and L-(alpha)amino acid structures as the alphabet. The molecular shapes accessible in de novo protein design are stereochemically defined. Indeed, the defining consideration for shape specificity in proteins to be alpha-helix/beta-sheet composites is the L configuration of the alpha-amino acid structures. The stereospecificity in shapes implies that protein shapes may be diversifiable stereochemically, that is, designable de novo, using D and L structures as the alphabet. Indeed, augmented with D enantiomers, Nature's alphabet will expand greatly in the diversity of polypeptide stereoisomers, for example, from 1(30) to 2(30)--that is, from one to ca. one billion--for a modestly sized 30-residue polypeptide. Furthermore, with each isomer having conformers stereospecific to its structure, molecular folds of specific shapes may be approachable sequentially when D and L structures are used as the alphabet. Illustrating the promise, 14-20-residue bracelet-, boat-, canoe-, and cup-shaped molecular folds were designed stereochemically or implemented as specific sequence plans in the D- and L-alpha-amino acid alphabet. In practical terms, canonical poly-L peptide folds were modified to the desired shapes via stereochemical mutations invoking enantiomer symmetries in the Ramachandran phi,psi space as the logic. For example, in designing the boat-shaped fold, the canonical beta-hairpin was reengineered in its flat planar structure via multiple coordinated L-to-D mutations in its position specific cross-strand neighbor residues, upturning its ends enclosing six side chains in a molecular cleft. While affirming the generality of the approach, the 20-residue molecular canoe and the 14-residue molecular cup are also presented as examples of the scope of functional design. The canoe, possessing alkali cation-specific catgrips in its main chain, and the cup, featuring an organic cation-specific aromatic triad in its side chains, do indeed display desired specificities in their ligand binding. Stereochemistry is, therefore, the crucial specifier of protein shapes and valuable as the tool for shape-specific protein design. Proteins in general, whether poly-L or mixed-D,L, require sequence effects of amino acid side chain structures for their stability, if not also for specifying them conformationally. The principles underlying these phenomena remain a puzzle, but studies invoking a stereochemical mutation approach to the problem have suggested that the poly-L structure may be crucial to the principles of sequential encoding of protein structures in amino acid side chains as the alphabet.

Scoring functions for de novo protein structure prediction revisited

De novo protein structure prediction methods attempt to predict tertiary structures from sequences based on general principles that govern protein folding energetics and/or statistical tendencies of conformational features that native structures acquire, without the use of explicit templates. A general paradigm for de novo prediction involves sampling the conformational space, guided by scoring functions and other sequence-dependent biases, such that a large set of candidate ("decoy") structures are generated, and then selecting native-like conformations from those decoys using scoring functions as well as conformer clustering. High-resolution refinement is sometimes used as a final step to fine-tune native-like structures. There are two major classes of scoring functions. Physics-based functions are based on mathematical models describing aspects of the known physics of molecular interaction. Knowledge-based functions are formed with statistical models capturing aspects of the properties of native protein conformations. We discuss the implementation and use of some of the scoring functions from these two classes for de novo structure prediction in this chapter.

Conformational landscape of the HIV-V3 hairpin loop from all-atom free-energy simulations

Small beta hairpins have many distinct biological functions, including their involvement in chemokine and viral receptor recognition. The relevance of structural similarities between different hairpin loops with near homologous sequences is not yet understood, calling for the development of methods for de novo hairpin structure prediction and simulation. De novo folding of beta strands is more difficult than that of helical proteins because of nonlocal hydrogen bonding patterns that connect amino acids that are distant in the amino acid sequence and there is a large variety of possible hydrogen bond patterns. Here we use a greedy version of the basin hopping technique with our free-energy forcefield PFF02 to reproducibly and predictively fold the hairpin structure of a HIV-V3 loop. We performed 20 independent basin hopping runs for 500 cycles corresponding to 7.4 x 10(7) energy evaluations each. The lowest energy structure found in the simulation has a backbone root mean square deviation (bRMSD) of only 2.04 A to the native conformation. The lowest 9 out of the 20 simulations converged to conformations deviating less than 2.5 A bRMSD from native.

Determination of conformational preferences of dipeptides using vibrational spectroscopy

The NMR coupling constants ((3)J(H(N), H(alpha))) of dipeptides indicate that the backbone conformational preferences vary strikingly among dipeptides. These preferences are similar to those of residues in small peptides, denatured proteins, and the coil regions of native proteins. Detailed characterization of the conformational preferences of dipeptides is therefore of fundamental importance for understanding protein structure and folding. Here, we studied the conformational preferences of 13 dipeptides using infrared and Raman spectroscopy. The main advantage of vibrational spectroscopy over NMR spectroscopy is in its much shorter time scale, which enables the determination of the conformational preferences of short-lived states. Accuracy of structure determination using vibrational spectroscopy depends critically on identification of the vibrational parameters that are sensitive to changes in conformation. We show that the frequencies of the amide I band and the A12 ratio of the amide I components of dipeptides correlate with the (3)J(H(N), H(alpha)). These two infrared vibrational parameters are thus analogous to (3)J(H(N), H(alpha)), indicators for the preference for the dihedral angle phi. We also show that the intensities of the components of the amide III bands in infrared spectra and the intensities of the skeletal vibrations in Raman spectra are indicators of populations of the P(II), beta, and alpha(R) conformations. The results show that alanine dipeptide adopts predominantly a PII conformation. The population of the beta conformation increases in valine dipeptides. The populations of the alpha(R) conformation are generally small. These data are in accord with the electrostatic screening model of conformational preferences.

Statistical theory for protein ensembles with designed energy landscapes

Combinatorial protein libraries provide a promising route to investigate the determinants and features of protein folding and to identify novel folding amino acid sequences. A library of sequences based on a pool of different monomer types are screened for folding molecules, consistent with a particular foldability criterion. The number of sequences grows exponentially with the length of the polymer, making both experimental and computational tabulations of sequences infeasible. Herein a statistical theory is extended to specify the properties of sequences having particular values of global energetic quantities that specify their energy landscape. The theory yields the site-specific monomer probabilities. A foldability criterion is derived that characterizes the properties of sequences by quantifying the energetic separation of the target state from low-energy states in the unfolded ensemble and the fluctuations of the energies in the unfolded state ensemble. For a simple lattice model of proteins, excellent agreement is observed between the theory and the results of exact enumeration. The theory may be used to provide a quantitative framework for the design and interpretation of combinatorial experiments.

Electrostatic screening and backbone preferences of amino acid residues in urea-denatured ubiquitin

Local structures in denatured proteins may be important in guiding a polypeptide chain during the folding and misfolding processes. Existence of local structures in chemically denatured proteins is a highly controversial issue. NMR parameters [coupling constants (3) J(H(alpha),H(N)) and chemical shifts] of chemically denatured proteins in general deviate little from their values in small peptides. These peptides were presumed to be completely unstructured; therefore, it was considered that chemically denatured proteins are random coils. But recent experimental studies show that small peptides adopt relatively stable structures in aqueous solutions. Small deviations of the NMR parameters from their values in small peptides may thus actually indicate the existence of local structures in chemically denatured proteins. Using NMR data and theoretical predictions we show here that fluctuating beta-strands exist in urea-denatured ubiquitin (8 M urea at pH 2). Residues in such beta-strands populate more frequently the left side of the broad beta region of -psi space. Urea-denatured ubiquitin contains no detectable beta-sheet secondary structures; nevertheless, the fluctuating beta-strands in urea-denatured ubiquitin coincide to the beta-strands in the native state. Formation of beta-strands is in accord with the electrostatic screening model of unfolded proteins. The free energy of a residue in an unfolded protein is in this model determined by the local backbone electrostatics and its screening by backbone solvation. These energy terms introduce strong electrostatic coupling between neighboring residues, which causes cooperative formation of beta-strands in denatured proteins. We propose that fluctuating beta-strands in denatured proteins may serve as initiation sites to form fibrils.

Energetics of protein folding

The energetics of protein folding determine the 3D structure of a folded protein. Knowledge of the energetics is needed to predict the 3D structure from the amino acid sequence or to modify the structure by protein engineering. Recent developments are discussed: major factors are reviewed and auxiliary factors are discussed briefly. Major factors include the hydrophobic factor (burial of non-polar surface area) and van der Waals interactions together with peptide hydrogen bonds and peptide solvation. The long-standing model for the hydrophobic factor (free energy change proportional to buried non-polar surface area) is contrasted with the packing-desolvation model and the approximate nature of the proportionality between free energy and apolar surface area is discussed. Recent energetic studies of forming peptide hydrogen bonds (gas phase) are reviewed together with studies of peptide solvation in solution. Closer agreement is achieved between the 1995 values for protein unfolding enthalpies in vacuum given by Lazaridis-Archontis-Karplus and Makhatadze-Privalov when the solvation enthalpy of the peptide group is taken from electrostatic calculations. Auxiliary factors in folding energetics include salt bridges and side-chain hydrogen bonds, disulfide bridges, and propensities to form alpha-helices and beta-structure. Backbone conformational entropy is a major energetic factor which is discussed only briefly for lack of knowledge.

Conformational Diversity of the Fibrillogenic Fusion Peptide B18 in Different Environments from Molecular Dynamics Simulations

The development of specific agents against amyloidoses requires an understanding of the conformational behavior of fibrillogenic peptides in different environments on the microscopic level. We present extensive molecular dynamics simulations of the fibrillogenic Bindin (103-120) B18 fusion peptide for several different environments: a water-trifluorethanol (TFE) mixture, pure water, aqueous buffer containing 100 mM NaCl, and a buffer-vapor interface. The peptide was studied as an isolated molecule in solution or at an interface. In the simulations, the conformational behavior of the peptide was found to strongly depend on the environment in agreement with experimental data. Overall, large portions of the peptide were unstructured. Preformed alpha-helical conformations were least stable in pure water and most stable in the water-TFE mixture and the buffer-vapor interface. In all environments, the alpha-helical conformation was most stable in the region around residues 113-116, which are mainly hydrophilic. Extended configurations in water or buffer folded into structures containing beta-sheets in agreement with data from circular dichroism spectroscopy. In buffer, the beta-sheet content was larger than in water and alpha-beta transitions were observed at elevated temperature. Beta-sheets were formed by hydrophobic residues; turns were formed by hydrophilic residues. A few typical beta-sheets that contain different residues are suggested. A B18 molecule in a strand-loop-strand conformation placed in buffer in contact with vapor was spontaneously adsorbed to the buffer-vapor interface with its hydrophobic side pointing toward the vapor phase. The adsorption induced the formation of turns at positions 108-119 and alpha-helical conformations in the region around residues 114-117. Alpha-helices were parallel to the interface plane in agreement with data from IR reflection absorption spectroscopy.

Protein structure prediction by all-atom free-energy refinement

Background

The reliable prediction of protein tertiary structure from the amino acid sequence remains challenging even for small proteins. We have developed an all-atom free-energy protein forcefield (PFF01) that we could use to fold several small proteins from completely extended conformations. Because the computational cost of de-novo folding studies rises steeply with system size, this approach is unsuitable for structure prediction purposes. We therefore investigate here a low-cost free-energy relaxation protocol for protein structure prediction that combines heuristic methods for model generation with all-atom free-energy relaxation in PFF01.

Results

We use PFF01 to rank and cluster the conformations for 32 proteins generated by ROSETTA. For 22/10 high-quality/low quality decoy sets we select near-native conformations with an average C_α root mean square deviation of 3.03 Å/6.04 Å. The protocol incorporates an inherent reliability indicator that succeeds for 78% of the decoy sets. In over 90% of these cases near-native conformations are selected from the decoy set. This success rate is rationalized by the quality of the decoys and the selectivity of the PFF01 forcefield, which ranks near-native conformations an average 3.06 standard deviations below that of the relaxed decoys (Z-score).

Conclusion

All-atom free-energy relaxation with PFF01 emerges as a powerful low-cost approach toward generic de-novo protein structure prediction. The approach can be applied to large all-atom decoy sets of any origin and requires no preexisting structural information to identify the native conformation. The study provides evidence that a large class of proteins may be foldable by PFF01.

Comparison of stochastic optimization methods for all-atom folding of the Trp-Cage protein

The performances of three different stochastic optimization methods for all-atom protein structure prediction are investigated and compared. We use the recently developed all-atom free-energy force field (PFF01), which was demonstrated to correctly predict the native conformation of several proteins as the global optimum of the free energy surface. The trp-cage protein (PDB-code 1L2Y) is folded with the stochastic tunneling method, a modified parallel tempering method, and the basin-hopping technique. All the methods correctly identify the native conformation, and their relative efficiency is discussed.

All-atomde novo protein folding with a scalable evolutionary algorithm

The search for efficient and predictive methods to describe the protein folding process at the all-atom level remains an important grand-computational challenge. The development of multi-teraflop architectures, such as the IBM BlueGene used in this study, has been motivated in part by the large computational requirements of such studies. Here we report the predictive all-atom folding of the forty-amino acid HIV accessory protein using an evolutionary stochastic optimization technique. We implemented the optimization method as a master-client model on an IBM BlueGene, where the algorithm scales near perfectly from 64 to 4096 processors in virtual processor mode. Starting from a completely extended conformation, we optimize a population of 64 conformations of the protein in our all-atom free-energy model PFF01. Using 2048 processors the algorithm predictively folds the protein to a near-native conformation with an RMS deviation of 3.43 A in < 24 h.

Energy landscape paving simulations of the trp-cage protein

We evaluate the efficiency of multiple variants of energy landscape paving in all-atom simulations of the trp-cage protein using a recently developed new force field. Especially, we introduce a temperature-free variant of the method and demonstrate that it allows a fast scanning of the energy landscape. Nativelike structures are found in less time than by other techniques. The sampled low-energy configurations indicate a funnel-like energy landscape.

Alpha-helix stabilization by alanine relative to glycine: roles of polar and apolar solvent exposures and of backbone entropy

The energetics of alpha-helix formation are fairly well understood and the helix content of a given amino acid sequence can be calculated with reasonable accuracy from helix-coil transition theories that assign to the different residues specific effects on helix stability. In internal helical positions, alanine is regarded as the most stabilizing residue, whereas glycine, after proline, is the more destabilizing. The difference in stabilization afforded by alanine and glycine has been explained by invoking various physical reasons, including the hydrophobic effect and the entropy of folding. Herein, the contribution of these two effects and that of hydrophilic area burial is evaluated by analyzing Ala and Gly mutants implemented in three helices of apoflavodoxin. These data, combined with available data for similar mutations in other proteins (22 Ala/Gly mutations in alpha-helices have been considered), allow estimation of the difference in backbone entropy between alanine and glycine and evaluation of its contribution and that of apolar and polar area burial to the helical stabilization typically associated to Gly-->Ala substitutions. Alanine consistently stabilizes the helical conformation relative to glycine because it buries more apolar area upon folding and because its backbone entropy is lower. However, the relative contribution of polar area burial (which is shown to be destabilizing) and of backbone entropy critically depends on the approximation used to model the structure of the denatured state. In this respect, the excised-peptide model of the unfolded state, proposed by Creamer and coworkers (1995), predicts a major contribution of polar area burial, which is in good agreement with recent quantitations of the relative enthalpic contribution of Ala and Gly residues to alpha-helix formation.

Diffusion-collision of foldons elucidates the kinetic effects of point mutations and suggests control strategies of the folding process of helical proteins

In this article we use mutation studies as a benchmark for a minimal model of the folding process of helical proteins. The model ascribes a pivotal role to the collisional dynamics of a few crucial residues (foldons) and predicts the folding rates by exploiting information drawn from the protein sequence. We show that our model rationalizes the effects of point mutations on the kinetics of folding. The folding times of two proteins and their mutants are predicted. Stability and location of foldons have a critical role as the determinants of protein folding. This allows us to elucidate two main mechanisms for the kinetic effects of mutations. First, it turns out that the mutations eliciting the most notable effects alter protein stability through stabilization or destabilization of the foldons. Secondly, the folding rate is affected via a modification of the foldon topology by those mutations that lead to the birth or death of foldons. The few mispredicted folding rates of some mutants hint at the limits of the current version of the folding model proposed in the present article. The performance of our folding model declines in case the mutated residues are subject to strong long-range forces. That foldons are the critical targets of mutation studies has notable implications for design strategies and is of particular interest to address the issue of the kinetic regulation of single proteins in the general context of the overall dynamics of the interactome.

Effect of organic solvents on the conformation and interaction of catalase and anticatalase antibodies

Effect of six organic solvents-methanol, ethanol, propanol, dimethyl sulphoxide (DMSO), N,N-dimethyl formamide (DMF), and glycerol on the conformation and interaction of catalase and anticatalase antibodies were studied with the aim of identifying the solvents in which antigen-antibody interactions are strong. The antigen binding activity of the antibodies in the various organic solvents increased in the following order: ethanol<methanol<no organic solvent<propanol<DMSO<DMF<glycerol. The structure of both the antibody and the antigen molecule was affected significantly in 40% concentration of the organic solvents used in this study. Catalase activity was inhibited in DMSO. However, the enzyme was activated in DMF upto about 50% of its concentration.

A new catalog of protein beta-sheets

Systematic protein folding studies depend on protein three-dimensional structure annotation, the assignment of amino acid structural types from atomic coordinates. Significant stabilizing factors between adjacent beta-sheet peptide chains have recently been characterized and were not considered during the development of previously published annotation methods. To produce an accurate beta-sheet domain catalog and to encompass the full beta-sheet spectacle, we developed a method, beta-Spider, which evaluates a packing energy between adjacent peptide chains in accordance with the newly discovered stabilizing factors. While considering important energetic factors, our approach also minimizes the use of subjective criteria, such as (phi,psi) boundaries and sets of H-bonding motifs that are used in other existing methods. As a result of the application of beta-Spider to a set of available high-resolution X-ray crystal structures, we present here a new beta-sheet catalog that differs considerably from the one produced by the most acclaimed DSSP method. The catalog includes new H-bonding motifs that were never reported.