Proteins: Structure, Function, Bioinformatics
Effect of Intrinsic and Extrinsic Factors on the Simulated D-band Length of Type I Collagen
A signature feature of collagen is its axial periodicity visible in TEM as alternating dark and light bands. In mature, type I collagen, this repeating unit, D, is 67 nm long. This periodicity reflects an underlying packing of constituent triple-helix polypeptide monomers wherein the dark bands represent gaps between axially adjacent monomers. This organization is visible distinctly in the microfibrillar model of collagen obtained from fiber diffraction. However, to date, no atomistic simulations of this diffraction model under zero-stress conditions have reported a preservation of this structural feature. Such a demonstration is important as it provides the baseline to infer response functions of physiological stimuli. In contrast, simulations predict a considerable shrinkage of the D-band (11-19%). Here we evaluate systemically the effect of several factors on D-band shrinkage. Using force fields employed in previous studies we find that irrespective of the temperature/pressure coupling algorithms, assumed salt concentration or hydration level, and whether or not the monomers are cross-linked, the D-band shrinks considerably. This shrinkage is associated with the bending and widening of individual monomers, but employing a force field whose backbone dihedral energy landscape matches more closely with our computed CCSD(T) values produces a small D-band shrinkage of < 3%. Since this force field also performs better against other experimental data, it appears that the large shrinkage observed in earlier simulations is a force-field artifact. The residual shrinkage could be due to the absence of certain atomic-level details, such as glycosylation sites, for which we do not yet have suitable data. This article is protected by copyright. All rights reserved.
Probing protease sensitivity of recombinant human erythropoietin reveals α3-α4 inter-helical loop as a stability determinant
Although unglycosylated HuEpo is fully functional, it has very short serum half-life. However, the mechanism of in vivo clearance of human Epo (HuEpo) remains largely unknown. In this study, the relative importance of protease-sensitive sites of recombinant HuEpo (rHuEpo) has been investigated by analysis of structural data coupled with in vivo half-life measurements. Our results identify α3-α4 inter-helical loop region as a target site of lysosomal protease Cathepsin L. Consistent with previously-reported lysosomal degradation of HuEpo, these results for the first time identify cleavage sites of rHuEpo by specific lysosomal proteases. Furthermore, in agreement with the lowered exposure of the peptide backbone around the cleavage site, remarkably substitutions of residues with bulkier amino acids result in significantly improved in vivo stability. Together, these results have implications for the mechanism of in vivo clearance of the protein in humans. This article is protected by copyright. All rights reserved.
In recent years in silico protein structure prediction reached a level where fully automated servers can generate large pools of near-native structures. However, the identification and further refinement of the best structures from the pool of models remain problematic. To address these issues, we have developed (i) a target-specific selective refinement (SR) protocol; and (ii) molecular dynamics (MD) simulation based ranking (SMDR) method. In SR the all-atom refinement of structures is accomplished via the Rosetta Relax protocol, subject to specific constraints determined by the size and complexity of the target. The best-refined models are selected with SMDR by testing their relative stability against gradual heating through all-atom MD simulations. Through extensive testing we have found that Mufold-MD, our fully automated protein structure prediction server updated with the SR and SMDR modules consistently outperformed its previous versions. This article is protected by copyright. All rights reserved.
Molecular dynamics simulations indicate that TyrosineB10 limits motions of distal Histidine to regulate CO binding in soybean leghemoglobin
Myoglobin (Mb) uses strong electrostatic interaction in its distal heme pocket to regulate ligand binding. The mechanism of regulation of ligand binding in soybean leghemoglobin a (Lba) has been enigmatic and more so due to the absence of gaseous ligand bound atomic resolution three-dimensional structure of the plant globin. While the 20-fold higher oxygen affinity of Lba compared to Mb is required for its dual physiological function, the mechanism by which this high affinity is achieved is only emerging. Extensive mutational analysis combined with kinetic and CO-FTIR spectroscopic investigation led to the hypothesis that Lba depended on weakened electrostatic interaction between distal HisE7 and bound ligand achieved by invoking B10Tyr, which itself hydrogen bonds with HisE7 thus restricting it in a single conformation detrimental to Mb-like strong electrostatic interaction. Such theory has been re-assessed here using CO-Lba in silico model and molecular dynamics simulation. The investigation supports the presence of at least two major conformations of HisE7 in Lba brought about by imidazole ring flip, one of which makes hydrogen bonds effectively with B10Tyr affecting the former's ability to stabilize bound ligand, while the other does not. However, HisE7 in Lba has limited conformational freedom unlike high frequency of imidazole ring flips observed in Mb and in TyrB10Leu mutant of Lba. Thus, it appears that TyrB10 limits the conformational freedom of distal His in Lba, tuning down ligand dissociation rate constant by reducing the strength of hydrogen bonding to bound ligand, which the freedom of distal His of Mb allows. This article is protected by copyright. All rights reserved.
CASP11 refinement experiments with ROSETTA
We report new Rosetta-based approaches to tackling the major issues that confound protein structure refinement, and the testing of these approaches in the CASP11 experiment. Automated refinement protocols were developed that integrate a range of sampling methods using parallel computation and multi-objective optimization. In CASP11, we used a more aggressive large scale structure rebuilding approach for poor starting models, and a less aggressive local rebuilding plus core refinement approach for starting models likely to be closer to the native structure. The more incorrectly modeled a structure was predicted to be, the more it was allowed to vary during refinement. The CASP11 experiment revealed strengths and weaknesses of the approaches: the high-resolution strategy incorporating local rebuilding with core refinement consistently improved starting structures, while the low-resolution strategy incorporating the reconstruction of large parts of the structures improved starting models in some cases but often considerably worsened them, largely because of model selection issues. Overall, the results suggest the high-resolution refinement protocol is a promising method orthogonal to other approaches, while the low-resolution refinement method clearly requires further development. This article is protected by copyright. All rights reserved.
Here we present the results of residue-residue contact predictions achieved in CASP11 by the CONSIP2 server, which is based around our MetaPSICOV contact prediction method. On a set of 40 target domains with a median family size of around 40 effective sequences, our server achieved an average top-L/5 long-range contact precision of 27%. MetaPSICOV method bases on a combination of classical contact prediction features, enhanced with three distinct coevolution methods embedded in a 2-stage neural network predictor. Some unique features of our approach are: (1) the tuning between the classical and coevolution features depending on the depth of the input alignment and (2) a hybrid approach to generate deepest possible multiple-sequence alignments by combining jackHMMer and HHblits. We discuss the CONSIP2 pipeline, our results and show that where the method underperformed, the major factor was relying on a fixed set of parameters for the initial sequence alignments and not attempting to perform domain splitting as a pre-processing step. This article is protected by copyright. All rights reserved.
Protein structures predicted by state-of-the-art template-based methods may still have errors when the template proteins are not similar enough to the target protein. Overall target structure may deviate from the template structures owing to differences in sequences. Structural information for some local regions such as loops may not be available when there are sequence insertions or deletions. Those structural aspects that originate from deviations from templates can be dealt with by ab initio structure refinement methods to further improve model accuracy. In the CASP11 refinement experiment, we tested three different refinement methods that utilize overall structure relaxation, loop modeling, and quality assessment of multiple initial structures. From this experiment, we conclude that the overall relaxation method can consistently improve model quality. Loop modeling is the most useful when the initial model structure is high quality, with GDT-HA >60. The method that used multiple initial structures further refined the already refined models; the minor improvements with this method raise the issue of problem with the current energy function. Future research directions are also discussed. Proteins 2015. © 2015 Wiley Periodicals, Inc.
Optimizing the affinity and specificity of ligand binding with the inclusion of solvation effect
Solvation effect is an important factor for protein–ligand binding in aqueous water. Previous scoring function of protein–ligand interactions rarely incorporates the solvation model into the quantification of protein–ligand interactions, mainly due to the immense computational cost, especially in the structure-based virtual screening, and nontransferable application of independently optimized atomic solvation parameters. In order to overcome these barriers, we effectively combine knowledge-based atom–pair potentials and the atomic solvation energy of charge-independent implicit solvent model in the optimization of binding affinity and specificity. The resulting scoring functions with optimized atomic solvation parameters is named as specificity and affinity with solvation effect (SPA-SE). The performance of SPA-SE is evaluated and compared to 20 other scoring functions, as well as SPA. The comparative results show that SPA-SE outperforms all other scoring functions in binding affinity prediction and “native” pose identification. Our optimization validates that solvation effect is an important regulator to the stability and specificity of protein–ligand binding. The development strategy of SPA-SE sets an example for other scoring function to account for the solvation effect in biomolecular recognitions. Proteins 2015. © 2015 Wiley Periodicals, Inc.
Allosteric transitions of ATP-binding cassette transporter MsbA studied by the adaptive anisotropic network model
The transporter MsbA is a kind of multidrug resistance ATP-binding cassette transporter that can transport lipid A, lipopolysaccharides, and some amphipathic drugs from the cytoplasmic to the periplasmic side of the inner membrane. In this work, we explored the allosteric pathway of MsbA from the inward- to outward-facing states during the substrate transport process with the adaptive anisotropic network model. The results suggest that the allosteric transitions proceed in a coupled way. The large-scale closing motions of the nucleotide-binding domains occur first, accompanied with a twisting motion at the same time, which becomes more obvious in middle and later stages, especially for the later. This twisting motion plays an important role for the rearrangement of transmembrane helices and the opening of transmembrane domains on the periplasmic side that mainly take place in middle and later stages respectively. The topological structure plays an important role in the motion correlations above. The conformational changes of nucleotide-binding domains are propagated to the transmembrane domains via the intracellular helices IH1 and IH2. Additionally, the movement of the transmembrane domains proceeds in a nonrigid body, and the two monomers move in a symmetrical way, which is consistent with the symmetrical structure of MsbA. These results are helpful for understanding the transport mechanism of the ATP-binding cassette exporters. Proteins 2015. © 2015 Wiley Periodicals, Inc.
Microsecond simulations of mdm2 and its complex with p53 yield insight into force field accuracy and conformational dynamics
The p53-MDM2 complex is both a major target for cancer drug development and a valuable model system for computational predictions of protein-ligand binding. To investigate the accuracy of molecular simulations of MDM2 and its complex with p53, we performed a number of long (200 ns to 1 µs) explicit-solvent simulations using a range of force fields. We systematically compared nine popular force fields (AMBER ff03, ff12sb, ff14sb, ff99sb, ff99sb-ildn, ff99sb-ildn-nmr, ff99sb-ildn-phi, CHARMM22*, and CHARMM36) against experimental chemical shift data, and found similarly accurate results, with microsecond simulations achieving better agreement compared to 200-ns trajectories. Although the experimentally determined apo structure has a closed binding cleft, simulations in all force fields suggest the apo state of MDM2 is highly flexible, and able to sample holo-like conformations, consistent with a conformational selection model. Initial structuring of the MDM2 lid region, known to competitively bind the binding cleft, is also observed in long simulations. Taken together, these results show molecular simulations can accurately sample conformations relevant for ligand binding. We expect this study to inform future computational work on folding and binding of MDM2 ligands. Proteins 2015. © 2015 Wiley Periodicals, Inc.
Protein structure refinement by optimization
Knowledge-based protein potentials are simplified potentials designed to improve the quality of protein models, which is important as more accurate models are more useful for biological and pharmaceutical studies. Consequently, knowledge-based potentials often are designed to be efficient in ordering a given set of deformed structures denoted decoys according to how close they are to the relevant native protein structure. This, however, does not necessarily imply that energy minimization of this potential will bring the decoys closer to the native structure. In this study, we introduce an iterative strategy to improve the convergence of decoy structures. It works by adding energy optimized decoys to the pool of decoys used to construct the next and improved knowledge-based potential. We demonstrate that this strategy results in significantly improved decoy convergence on Titan high resolution decoys and refinement targets from Critical Assessment of protein Structure Prediction competitions. Our potential is formulated in Cartesian coordinates and has a fixed backbone potential to restricts motions to be close to those of a dihedral model, a fixed hydrogen-bonding potential and a variable coarse grained carbon alpha potential consisting of a pair potential and a novel solvent potential that are b-spline based as we use explicit gradient and Hessian for efficient energy optimization. Proteins 2015. © 2015 Wiley Periodicals, Inc.
The metabolism of microbial organisms and its diversity are partly the result of an adaptation process to the characteristics of the environments that they inhabit. In this work, we analyze the influence of lifestyle on the content of promiscuous enzymes in 761 nonredundant bacterial and archaeal genomes. Promiscuous enzymes were defined as those proteins whose catalytic activities are defined by two or more different Enzyme Commission (E.C.) numbers. The genomes analyzed were categorized into four lifestyles for their exhaustive comparisons: free-living, extremophiles, pathogens, and intracellular. From these analyses we found that free-living organisms have larger genomes and an enrichment of promiscuous enzymes. In contrast, intracellular organisms showed smaller genomes and the lesser proportion of promiscuous enzymes. On the basis of our data, we show that the proportion of promiscuous enzymes in an organism is mainly influenced by the lifestyle, where fluctuating environments promote its emergence. Finally, we evidenced that duplication processes occur preferentially in metabolism of free-living and extremophiles species. Proteins 2015. © 2015 Wiley Periodicals, Inc.
Solution NMR and molecular dynamics reveal a persistent alpha helix within the dynamic region of PsbQ from photosystem II of higher plants
The extrinsic proteins of photosystem II of higher plants and green algae PsbO, PsbP, PsbQ, and PsbR are essential for stable oxygen production in the oxygen evolving center. In the available X-ray crystallographic structure of higher plant PsbQ residues S14-Y33 are missing. Building on the backbone NMR assignment of PsbQ, which includes this “missing link”, we report the extended resonance assignment including side chain atoms. Based on nuclear Overhauser effect spectra a high resolution solution structure of PsbQ with a backbone RMSD of 0.81 Å was obtained from torsion angle dynamics. Within the N-terminal residues 1–45 the solution structure deviates significantly from the X-ray crystallographic one, while the four-helix bundle core found previously is confirmed. A short α-helix is observed in the solution structure at the location where a β-strand had been proposed in the earlier crystallographic study. NMR relaxation data and unrestrained molecular dynamics simulations corroborate that the N-terminal region behaves as a flexible tail with a persistent short local helical secondary structure, while no indications of forming a β-strand are found. Proteins 2015. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.
Pauling's mastery of peptide stereochemistry—based on small molecule crystal structures and the theory of chemical bonding—led to his realization that the peptide unit is planar and then to the Pauling–Corey–Branson model of the α-helix. Similarly, contemporary protein structure refinement is based on experimentally determined diffraction data together with stereochemical restraints. However, even an X-ray structure at ultra-high resolution is still an under-determined model in which the linkage among refinement parameters is complex. Consequently, restrictions imposed on any given parameter can affect the entire structure. Here, we examine recent studies of high resolution protein X-ray structures, where substantial distortions of the peptide plane are found to be commonplace. Planarity is assessed by the ω-angle, a dihedral angle determined by the peptide bond (CN) and its flanking covalent neighbors; for an ideally planar trans peptide, ω = 180°. By using a freely available refinement package, Phenix [Afonine et al. (2012) Acta Cryst. D, 68:352–367], we demonstrate that tightening default restrictions on the ω-angle can significantly reduce apparent deviations from peptide unit planarity without consequent reduction in reported evaluation metrics (e.g., R-factors). To be clear, our result does not show that substantial non-planarity is absent, only that an equivalent alternative model is possible. Resolving this disparity will ultimately require improved understanding of the deformation energy. Meanwhile, we urge inclusion of ω-angle statistics in new structure reports in order to focus critical attention on the usual practice of assigning default values to ω-angle constraints during structure refinement. Proteins 2015. © 2015 Wiley Periodicals, Inc.
Upon being released from the N-terminal domain (NTD), the C-terminal domain (CTD) switches from α-helix conformation to β-barrel conformation, which converts RfaH from a transcription factor into an activator of translation. The conformational change may be viewed as allosteric transition. We use molecular dynamics simulations of coarse-grained off-lattice model to study the thermal folding of NTD, CTD, RfaH and the allosteric transition in CTD. The melting temperatures from the specific heat profiles indicate that the β-barrel conformation is much more stable than the α-helix conformation. Two helices in α-helix conformation have similar thermodynamic stabilities and the melting temperatures for β sheets show slight dispersion. Under the interaction with NTD, CTD is greatly stabilized and the cooperativity for thermal folding is also significantly improved. The allosteric transition can be approximately described by a two-state model and three parallel pathways are identified. The transition state ensemble, quantified by a Tanford β-like parameter, resembles the α-helix and β-barrel conformations almost to the same extent. Proteins 2015;. © 2015 Wiley Periodicals, Inc.
Despite recent improvements in computational methods for protein design, we still lack a quantitative, predictive understanding of the intrinsic probabilities for amino acids to adopt particular side-chain conformations. Surprisingly, this question has remained unsettled for many years, in part because of inconsistent results from different experimental approaches. To explicitly determine the relative populations of different side-chain dihedral angles, we performed all-atom hard-sphere Langevin Dynamics simulations of leucine (Leu) and isoleucine (Ile) dipeptide mimetics with stereo-chemical constraints and repulsive-only steric interactions between non-bonded atoms. We determine the relative populations of the different χ1 and χ2 dihedral angle combinations as a function of the backbone dihedral angles ϕ and ψ. We also propose, and test, a mechanism for inter-conversion between the different side-chain conformations. Specifically, we discover that some of the transitions between side-chain dihedral angle combinations are very frequent, whereas others are orders of magnitude less frequent, because they require rare coordinated motions to avoid steric clashes. For example, to transition between different values of χ2, the Leu side-chain bond angles κ1 and κ2 must increase, whereas to transition in χ1, the Ile bond angles λ1 and λ2 must increase. These results emphasize the importance of computational approaches in stimulating further experimental studies of the conformations of side-chains in proteins. Moreover, our studies emphasize the power of simple steric models to inform our understanding of protein structure, dynamics, and design. Proteins 2015; 83:1488–1499. © 2015 Wiley Periodicals, Inc.
Allosteric sites can be identified based on the residue–residue interaction energy difference
Allosteric drugs act at a distance to regulate protein functions. They have several advantages over conventional orthosteric drugs, including diverse regulation types and fewer side effects. However, the rational design of allosteric ligands remains a challenge, especially when it comes to the identification allosteric binding sites. As the binding of allosteric ligands may induce changes in the pattern of residue–residue interactions, we calculated the residue–residue interaction energies within the allosteric site based on the molecular mechanics generalized Born surface area energy decomposition scheme. Using a dataset of 17 allosteric proteins with structural data for both the apo and the ligand-bound state available, we used conformational ensembles generated by molecular dynamics simulations to compute the differences in the residue–residue interaction energies in known allosteric sites from both states. For all the known sites, distinct interaction energy differences (>25%) were observed. We then used CAVITY, a binding site detection program to identify novel putative allosteric sites in the same proteins. This yielded a total of 31 “druggable binding sites,” of which 21 exhibited >25% difference in residue interaction energies, and were hence predicted as novel allosteric sites. Three of the predicted allosteric sites were supported by recent experimental studies. All the predicted sites may serve as novel allosteric sites for allosteric ligand design. Our study provides a computational method for identifying novel allosteric sites for allosteric drug design. Proteins 2015; 83:1375–1384. © 2014 Wiley Periodicals, Inc.
Structural and functional analysis of SleL, a peptidoglycan lysin involved in germination of Bacillus spores
A major event in the germination of Bacillus spores concerns hydrolysis of the cortical peptidoglycan that surrounds the spore protoplast, the integrity of which is essential for maintenance of dormancy. Cortex degradation is initiated in all species of Bacillus spores by the combined activity of two semi-redundant cortex-lytic enzymes, SleB and CwlJ. A third enzyme, SleL, which has N-acetylglucosaminidase activity, cleaves peptidoglycan fragments generated by SleB and CwlJ. Here we present crystal structures of B. cereus and B. megaterium SleL at 1.6 angstroms and 1.7 angstroms, respectively. The structures were determined with a view to identifying the structural basis of differences in catalytic efficiency between the respective enzymes. The catalytic (α/β)8-barrel cores of both enzymes are highly conserved from a structural perspective, including the spatial distribution of the catalytic residues. Both enzymes are equipped with two N-terminal peptidoglycan-binding LysM domains, which are also structurally highly conserved. However, the topological arrangement of the respective enzymes second LysM domain is markedly different, and this may account for differences in catalytic rates by impacting upon the position of the active sites with respect to their substrates. A chimeric enzyme comprising the B. megaterium SleL catalytic domain plus B. cereus SleL LysM domains displayed enzymatic activity comparable to the native B. cereus protein, exemplifying the importance of the LysM domains to SleL function. Similarly, the reciprocal construct, comprising the B. cereus SleL catalytic domain with B. megaterium SleL LysM domains, showed reduced activity compared to native B. cereus SleL. This article is protected by copyright. All rights reserved.
Restricted mobility of side chains on concave surfaces of solenoid proteins may impart heightened potential for intermolecular interactions
Significant progress has been made in the determination of the protein structures with their number today passing over a hundred thousand structures. The next challenge is the understanding and prediction of protein–protein and protein–ligand interactions. In this work we address this problem by analyzing curved solenoid proteins. Many of these proteins are considered as “hub molecules” for their high potential to interact with many different molecules and to be a scaffold for multisubunit protein machineries. Our analysis of these structures through molecular dynamics simulations reveals that the mobility of the side-chains on the concave surfaces of the solenoids is lower than on the convex ones. This result provides an explanation to the observed preferential binding of the ligands, including small and flexible ligands, to the concave surface of the curved solenoid proteins. The relationship between the landscapes and dynamic properties of the protein surfaces can be further generalized to the other types of protein structures and eventually used in the computer algorithms, allowing prediction of protein–ligand interactions by analysis of protein surfaces. Proteins 2015. © 2015 Wiley Periodicals, Inc.
Crystal structure of A. aeolicus LpxC with bound product suggests alternate deacetylation mechanism
UDP-3-O-acyl-N-acetylglucosamine deacetylase (LpxC) is the first committed step to form lipid A, an essential component of the outer membrane of Gram-negative bacteria. As it is essential for the survival of many pathogens, LpxC is an attractive target for antibacterial therapeutics. Herein we report the product-bound co-crystal structure of LpxC from the acheal Aquifex aeolicus solved to 1.6 Å resolution. We identified interactions by hydroxyl and hydroxymethyl substituents of the product glucosamine ring that may enable new insights to exploit waters in the active site for structure-based design of LpxC inhibitors with novel scaffolds. By utilizing this product structure, we have performed quantum mechanical modeling on the substrate in the active site. Based on our results and published experimental data, we propose a new mechanism that may lead to a better understanding of LpxC catalysis and inhibition. This article is protected by copyright. All rights reserved.