Nonplanar peptide bonds in proteins are common and conserved but not biased toward active sites

Enantiomeric purity of synthetic therapeutic peptides: A review

Synthetic therapeutic peptides are a complex and popular class of pharmaceuticals. In recent years, peptides with proven therapeutic activity have gained significant interest in the market. The determination of synthetic peptide enantiomeric purity plays a critical role in the evaluation of the quality of the medicine. Since racemization is one of the most common side reactions occurring in AAs or peptides, enantiomeric impurities such as D-isomers can form during the peptide synthesis or can be introduced from the starting materials (e.g., AAs). The therapeutic effect of a synthetic or semi-synthetic bioactive peptide molecule depends on its AA enantiomeric purity and secondary/tertiary structure. Therefore, the enantiomeric purity determination for synthetic peptides is supportive for interpreting unwanted therapeutic effects and determining the quality of synthetic peptide therapeutics. However, enantiomeric purity analysis encounters formidable analytical challenges during chromatographic separation, as D/L isomers have identical physical-chemical properties except stereochemical configuration. To ensure peptides AA stereochemical configuration whether in the free or bound state, sensitive and reproducible quantitative analytical method is mandatory. In this regard, numerous analytical techniques were emerged for the quantification of D-isomeric impurities in synthetic peptides, but still, very few reports are available in the literature. Thus, the purpose of this paper is to provide an overview of the importance, regulatory requirements, and various analytical methods used for peptide enantiomeric purity determination. In addition, we discussed the available literature in terms of enantiomeric impurity detection, common hydrolysis procedural aspects, and different analytical strategies used for sample preparation.

Learning Correlations between Internal Coordinates to Improve 3D Cartesian Coordinates for Proteins

We consider a generic representation problem of internal coordinates (bond lengths, valence angles, and dihedral angles) and their transformation to 3-dimensional Cartesian coordinates of a biomolecule. We show that the internal-to-Cartesian process relies on correctly predicting chemically subtle correlations among the internal coordinates themselves, and learning these correlations increases the fidelity of the Cartesian representation. We developed a machine learning algorithm, Int2Cart, to predict bond lengths and bond angles from backbone torsion angles and residue types of a protein, which allows reconstruction of protein structures better than using fixed bond lengths and bond angles or a static library method that relies on backbone torsion angles and residue types in a local environment. The method is able to be used for structure validation, as we show that the agreement between Int2Cart-predicted bond geometries and those from an AlphaFold 2 model can be used to estimate model quality. Additionally, by using Int2Cart to reconstruct an IDP ensemble, we are able to decrease the clash rate during modeling. The Int2Cart algorithm has been implemented as a publicly accessible python package at https://github.com/THGLab/int2cart.

Structural Basis for (2R,3R)-Taxifolin Binding and Reaction Products to the Bacterial Chalcone Isomerase of Eubacterium ramulus

The bacterial chalcone isomerase (CHI) from Eubacterium ramulus catalyses the first step in a flavanone-degradation pathway by a reverse Michael addition. The overall fold and the constitution of the active site of the enzyme completely differ from the well-characterised chalcone isomerase of plants. For (+)-taxifolin, CHI catalyses the intramolecular ring contraction to alphitonin. In this study, Fwe perform crystal structure analyses of CHI and its active site mutant His33Ala in the presence of the substrate taxifolin at 2.15 and 2.8 Å resolution, respectively. The inactive enzyme binds the substrate (+)-taxifolin as well defined, whereas the electron density maps of the native CHI show a superposition of substrate, product alphitonin, and most probably also the reaction intermediate taxifolin chalcone. Evidently, His33 mediates the stereospecific acid-base reaction by abstracting a proton from the flavonoid scaffold. The stereospecificity of the product is discussed.

Effect of Disulfide Bridge on the Binding of SARS-CoV-2 Fusion Peptide to Cell Membrane: A Coarse-Grained Study

In this paper, we present the parameterization of the CAVS coarse-grained (CG) force field for 20 amino acids, and our CG simulations show that the CAVS force field could accurately predict the amino acid tendency of the secondary structure. Then, we used the CAVS force field to investigate the binding of a severe acute respiratory syndrome-associated coronavirus fusion peptide (SARS-CoV-2 FP) to a phospholipid bilayer: a long FP (FP-L) containing 40 amino acids and a short FP (FP-S) containing 26 amino acids. Our CAVS CG simulations displayed that the binding affinity of the FP-L to the bilayer is higher than that of the FP-S. We found that the FP-L interacted more strongly with membrane cholesterol than the FP-S, which should be attributed to the stable helical structure of the FP-L at the C-terminus. In addition, we discovered that the FP-S had one major and two minor membrane-bound states, in agreement with previous all-atom molecular dynamics (MD) studies. However, we found that both the C-terminal and N-terminal amino acid residues of the FP-L can strongly interact with the bilayer membrane. Furthermore, we found that the disulfide bond formed between Cys840 and Cys851 stabilized the helices of the FP-L at the C-terminus, enhancing the interaction between the FP-L and the bilayer membrane. Our work indicates that the stable helical structure is crucial for binding the SARS-CoV-2 FP to cell membranes. In particular, the helical stability of FP should have a significant influence on the FP-membrane binding.

Identification of Single Amino Acid Chiral and Positional Isomers Using an Electrostatically Asymmetric Nanopore

Chirality is essential in nearly all biological organizations and chemical reactions but is rarely considered due to technical limitations in identifying L/D isomerization. Using OmpF, a membrane channel from Escherichia coli with an electrostatically asymmetric constriction zone, allows discriminating chiral amino acids in a single peptide. The heterogeneous distribution of charged residues in OmpF causes a strong lateral electrostatic field at the constriction. This laterally asymmetric constriction zone forces the sidechains of the peptides to specific orientations within OmpF, causing distinct ionic current fluctuations. Using statistical analysis of the respective ionic current variations allows distinguishing the presence and position of a single amino acid with different chiralities. To explore potential applications, the disease-related peptide β-Amyloid and its d-Asp¹ isoform and a mixture of the icatibant peptide drug (HOE 140) and its d-Ser⁷ mutant have been discriminated. Both chiral isomers were not applicable to be distinguished by mass spectroscopy approaches. These findings highlight a novel sensing mechanism for identifying single amino acids in single peptides and even for achieving single-molecule protein sequencing.

Revisiting the concept of peptide bond planarity in an iron-sulfur protein by neutron structure analysis

The planarity of the peptide bond is important for the stability and structure formation of proteins. However, substantial distortion of peptide bonds has been reported in several high-resolution structures and computational analyses. To investigate the peptide bond planarity, including hydrogen atoms, we report a 1.2-Å resolution neutron structure of the oxidized form of high-potential iron-sulfur protein. This high-resolution neutron structure shows that the nucleus positions of the amide protons deviate from the peptide plane and shift toward the acceptors. The planarity of the H─N─C═O plane depends strongly on the pyramidalization of the nitrogen atom. Moreover, the orientation of the amide proton of Cys⁷⁵ is different in the reduced and oxidized states, possibly because of the electron storage capacity of the iron-sulfur cluster.

Extension of the CAVS model to the simulation of helical peptides in a membrane environment

Considering the effect of peptide insertion on the dipole potential of the lipid membrane, we extend the CAVS coarse-grained (CG) model to the simulation of helical peptides in a membrane environment. In this approach, the CG scheme for a peptide backbone is similar to the treatment in the united-atom model, while we treated the side chain of an amino acid by grouping 1-3 heavy atoms into a CG unit. The CAVS CG force field for peptides is optimized by reproducing the experimental results for the backbone (φ, ψ) distribution and predicting the PMF profiles of transferring organic molecules in a lipid bilayer membrane obtained from all-atom simulations. The CAVS simulation of a helical peptide in a phosphatidylcholine (PC) lipid bilayer revealed that the insertion of a peptide increases the dipole potential of the PC lipid bilayer, in which the peptide and its neutralized ions make a significant contribution. Finally, we carried out the CAVS simulation for five different helical peptides in the PC lipid bilayer to explore the behavior of peptide tilt, showing excellent agreement with the all-atom simulations. Our work suggests that the peptide tilt should relieve the deformation stress from the lipid bilayer, and the peptide aggregation could reduce the peptide tilt by resisting the deformation stress from the surrounding lipids.

Comparative Physical Study of Three Pharmaceutically Active Benzodiazepine Derivatives: Crystalline versus Amorphous State and Crystallization Tendency

Chemical derivatization and amorphization are two possible strategies to improve the solubility and bioavailability of drugs, which is a key issue for the pharmaceutical industry. In this contribution, we explore whether both strategies can be combined by studying how small differences in the molecular structure of three related pharmaceutical compounds affect their crystalline structure and melting point (T_m), the relaxation dynamics in the amorphous phase, and the glass transition temperature (T_g), as well as the tendency toward recrystallization. Three benzodiazepine derivatives of almost same molecular mass and structure (Diazepam, Nordazepam and Tetrazepam) were chosen as model compounds. Nordazepam is the only one that displays N–H···O hydrogen bonds both in crystalline and amorphous phases, which leads to a significantly higher T_m (by 70–80 K) and T_g (by 30–40 K) compared to those of Tetrazepam and Diazepam (which display similar values of characteristic temperatures). The relaxation dynamics in the amorphous phase, as determined experimentally using broadband dielectric spectroscopy, is dominated by a structural relaxation and a Johari–Goldstein secondary relaxation, both of which scale with the reduced temperature T/T_g. The kinetic fragility index is very low and virtually the same (m_p ≈ 32) in all three compounds. Two more secondary relaxations are observed in the glass state: the slower of the two has virtually the same relaxation time and activation energy in all three compounds, and is assigned to the inter-enantiomer conversion dynamics of the flexible diazepine heterocycle between isoenergetic P and M conformations. We tentatively assign the fastest secondary relaxation, present only in Diazepam and Tetrazepam, to the rigid rotation of the fused diazepine–benzene double ring relative to the six-membered carbon ring. Such motion appears to be largely hindered in glassy Nordazepam, possibly due to the presence of the hydrogen bonds. Supercooled liquid Tetrazepam and Nordazepam are observed to crystallize into their stable crystalline form with an Avrami exponent close to unity indicating unidimensional growth with only sporadic nucleation, which allows a direct assessment of the crystal growth rate. Despite the very similar growth mode, the two derivatives exhibit very different kinetics for a fixed value of the reduced temperature and thus of the structural relaxation time, with Nordazepam displaying slower growth kinetics. Diazepam does not instead display any tendency toward recrystallization over short periods of time (even close to T_m). Both these observations in three very similar diazepine derivatives provide direct evidence that the kinetics of recrystallization of amorphous pharmaceuticals is not a universal function, at least in the supercooled liquid phase, of the structural or the conformational relaxation dynamics, and it is not simply correlated with related parameters such as the kinetic fragility or activation barrier of the structural relaxation. Only the crystal growth rate, and not the nucleation rate, shows a correlation with the presence or absence of hydrogen bonding.

A complete Fourier-synthesis-based backbone-conformation-dependent library for proteins

While broadening the applicability of (φ/ψ)-dependent target values for the bond angles in the peptide backbone, sequence/conformation categories with too few residues to analyze via previous methods were encountered. Here, a method of describing a conformation-dependent library (CDL) using two-dimensional Fourier coefficients is reported where the number of coefficients for individual categories is determined via complete cross-validation. Sample sizes are increased further by selective blending of categories with similar patterns of conformational dependence. An additional advantage of the Fourier-synthesis-based CDL is that it uses continuous functions and has no artifactual steps near the edges of populated regions of φ/ψ space. A set of libraries for the seven main-chain bond angles, along with the ω and ζ angles, was created based on a set of Fourier analyses of 48 368 residues selected from high-resolution models in the wwPDB. This new library encompasses both trans- and cis-peptide bonds and outperforms currently used discrete CDLs.

Mirror-image antiparallel β-sheets organize water molecules into superstructures of opposite chirality

Biomolecular hydration is fundamental to biological functions. Using phase-resolved chiral sum-frequency generation spectroscopy (SFG), we probe molecular architectures and interactions of water molecules around a self-assembling antiparallel β-sheet protein. We find that the phase of the chiroptical response from the O-H stretching vibrational modes of water flips with the absolute chirality of the (l-) or (d-) antiparallel β-sheet. Therefore, we can conclude that the (d-) antiparallel β-sheet organizes water solvent into a chiral supermolecular structure with opposite handedness relative to that of the (l-) antiparallel β-sheet. We use molecular dynamics to characterize the chiral water superstructure at atomic resolution. The results show that the macroscopic chirality of antiparallel β-sheets breaks the symmetry of assemblies of surrounding water molecules. We also calculate the chiral SFG response of water surrounding (l-) and (d-) LK₇β to confirm the presence of chiral water structures. Our results offer a different perspective as well as introduce experimental and computational methodologies for elucidating hydration of biomacromolecules. The findings imply potentially important but largely unexplored roles of water solvent in chiral selectivity of biomolecular interactions and the molecular origins of homochirality in the biological world.

A Proline-Based Tectons and Supramolecular Synthons for Drug Design 2.0: A Case Study of ACEI

Proline is a unique, endogenous amino acid, prevalent in proteins and essential for living organisms. It is appreciated as a tecton for the rational design of new bio-active substances. Herein, we present a short overview of the subject. We analyzed 2366 proline-derived structures deposited in the Cambridge Structure Database, with emphasis on the angiotensin-converting enzyme inhibitors. The latter are the first-line antihypertensive and cardiological drugs. Their side effects prompt a search for improved pharmaceuticals. Characterization of tectons (molecular building blocks) and the resulting supramolecular synthons (patterns of intermolecular interactions) involving proline derivatives, as presented in this study, may be useful for in silico molecular docking and macromolecular modeling studies. The DFT, Hirshfeld surface and energy framework methods gave considerable insight into the nature of close inter-contacts and supramolecular topology. Substituents of proline entity are important for the formation and cooperation of synthons. Tectonic subunits contain proline moieties characterized by diverse ionization states: -N and -COOH(-COO-), -N+ and -COOH(-COO-), -NH and -COOH(-COO-), -NH+ and -COOH(-COO-), and -NH2+ and -COOH(-COO-). Furthermore, pharmacological profiles of ACE inhibitors and their impurities were determined via an in silico approach. The above data were used to develop comprehensive classification, which may be useful in further drug design studies.

Numerous severely twisted N-acetylglucosamine conformations found in the protein databank

Taking advantage of the known planarity of the N-acetyl group of N-acetylglucosamine, an analysis of the quality of carbohydrate structures found in the protein databank was performed. Few obvious defects of the local geometry of the carbonyl group were observed. However, the N-acetyl group was often found in the less favorable cis conformation (12% of the cases). It was also found severely twisted in numerous instances, especially in structures with a resolution poorer than 1.9 Å determined between 2000 and 2015. Though the automated PDB-REDO procedure has proved able to improve nearly 85% of the structural models deposited to the PDB, and does prove able to cure most severely twisted conformations of the N-acetyl group, it fails to correct its high rate of cis conformations. More generally, for structures with a resolution poorer than 1.6 Å, it produces N-acetylglucosamine models in slightly poorer agreement with experimental data, as measured using real-space correlation coefficients. Significant improvements are thus still needed, at least as far as this carbohydrate structure is concerned.

Systematic Exploration of Protein Conformational Space Using a Distance Geometry Approach

The optimization approaches classically used during the determination of protein structure encounter various difficulties, especially when the size of the conformational space is large. Indeed, in such a case, algorithmic convergence criteria are more difficult to set up. Moreover, the size of the search space makes it difficult to achieve a complete exploration. The interval branch-and-prune (iBP) approach, based on the reformulation of the distance geometry problem (DGP) provides a theoretical frame for the generation of protein conformations, by systematically sampling the conformational space. When an appropriate subset of interatomic distances is known exactly, this worst-case exponential-time algorithm is provably complete and fixed-parameter tractable. These guarantees, however, immediately disappear as distance measurement errors are introduced. Here we propose an improvement of this approach: threading-augmented interval branch-and-prune (TAiBP), where the combinatorial explosion of the original iBP approach arising from its exponential complexity is alleviated by partitioning the input instances into consecutive peptide fragments and by using self-organizing maps (SOMs) to obtain clusters of similar solutions. A validation of the TAiBP approach is presented here on a set of proteins of various sizes and structures. The calculation inputs are a uniform covalent geometry extracted from force field covalent terms, the backbone dihedral angles with error intervals, and a few long-range distances. For most of the proteins smaller than 50 residues and interval widths of 20°, the TAiBP approach yielded solutions with RMSD values smaller than 3 Å with respect to the initial protein conformation. The efficiency of the TAiBP approach for proteins larger than 50 residues will require the use of nonuniform covalent geometry and may have benefits from the recent development of residue-specific force-fields.

Stereochemical Assessment of (φ,ψ) Outliers in Protein Structures Using Bond Geometry-Specific Ramachandran Steric-Maps

Ramachandran validation of protein structures is commonly performed using developments, such as MolProbity. We suggest tailoring such analyses by position-wise, geometry-specific steric-maps, which show (φ,ψ) regions with steric-clash at every residue position. These maps are different from the classical steric-map because they are highly sensitive to bond length and angle values that are used, in our steric-maps, as observed in the residue positions in super-high-resolution peptide and protein structures. (φ,ψ) outliers observed in such structures seldom have steric-clash. Therefore, we propose that a (φ,ψ) outlier is unacceptable if it is located within the steric-clash region of a bond geometry-specific steric-map for a residue position. These steric-maps also suggest position-specific accessible (φ,ψ) space. The PARAMA web resource performs in-depth position-wise analysis of protein structures using bond geometry-specific steric-maps.

A benchmark study of loop modeling methods applied to G protein-coupled receptors

G protein-coupled receptors (GPCR) are important drug discovery targets. Despite progress, many GPCR structures have not yet been solved. For these targets, comparative modeling is used in virtual ligand screening to prioritize experimental efforts. However, the structure of extracellular loop 2 (ECL2) is often poorly predicted. This is significant due to involvement of ECL2 in ligand binding for many Class A GPCR. Here we examine the performance of loop modeling protocols available in the Rosetta (cyclic coordinate descent [CCD], KIC with fragments [KICF] and next generation KIC [NGK]) and Molecular Operating Environment (MOE) software suites (de novo search). ECL2 from GPCR crystal structures served as the structure prediction targets and were divided into four sets depending on loop length. Results suggest that KICF and NGK sampled and scored more loop models with sub-angstrom and near-atomic accuracy than CCD or de novo search for loops of 24 or fewer residues. None of the methods were able to sample loop conformations with near-atomic accuracy for the longest targets ranging from 25 to 32 residues based on 1000 models generated. For these long loop targets, increased conformational sampling is necessary. The strongly conserved disulfide bond between Cys3.25 and Cys45.50 in ECL2 proved an effective filter. Setting an upper limit of 5.1 Å on the S-S distance improved the lowest RMSD model included in the top 10 scored structures in Groups 1-4 on average between 0.33 and 1.27 Å. Disulfide bond formation and geometry optimization of ECL2 provided an additional incremental benefit in structure quality.

The characterization of Thermotoga maritima Arginine Binding Protein variants demonstrates that minimal local strains have an important impact on protein stability

The Ramachandran plot is a versatile and valuable tool that provides fundamental information for protein structure determination, prediction, and validation. The structural/thermodynamic effects produced by forcing a residue to adopt a conformation predicted to be forbidden were here explored using Thermotoga maritima Arginine Binding Protein (TmArgBP) as model. Specifically, we mutated TmArgBP Gly52 that assumes a conformation believed to be strictly disallowed for non-Gly residues. Surprisingly, the crystallographic characterization of Gly52Ala TmArgBP indicates that the structural context forces the residue to adopt a non-canonical conformation never observed in any of the high-medium resolution PDB structures. Interestingly, the inspection of this high resolution structure demonstrates that only minor alterations occur. Nevertheless, experiments indicate that Gly52 replacements in TmArgBP produce destabilizations comparable to those observed upon protein truncation or dissection in domains. Notably, we show that force-fields commonly used in computational biology do not reproduce this non-canonical state. Using TmArgBP as model system we here demonstrate that the structural context may force residues to adopt conformations believed to be strictly forbidden and that barely detectable alterations produce major destabilizations. Present findings highlight the role of subtle strains in governing protein stability. A full understanding of these phenomena is essential for an exhaustive comprehension of the factors regulating protein structures.

Model validation: local diagnosis, correction and when to quit

Traditionally, validation was considered to be a final gatekeeping function, but refinement is smoother and results are better if model validation actively guides corrections throughout structure solution. This shifts emphasis from global to local measures: primarily geometry, conformations and sterics. A fit into the wrong local minimum conformation usually produces outliers in multiple measures. Moving to the right local minimum should be prioritized, rather than small shifts across arbitrary borderlines. Steric criteria work best with all explicit H atoms. `Backrub' motions should be used for side chains and `P-perp' diagnostics to correct ribose puckers. A `water' may actually be an ion, a relic of misfitting or an unmodeled alternate. Beware of wishful thinking in modeling ligands. At high resolution, internally consistent alternate conformations should be modeled and geometry in poor density should not be downweighted. At low resolution, CaBLAM should be used to diagnose protein secondary structure and ERRASER to correct RNA backbone. All atoms should not be forced inside density, beware of sequence misalignment, and very rare conformations such as cis-non-Pro peptides should be avoided. Automation continues to improve, but the crystallographer still must look at each outlier, in the context of density, and correct most of them. For the valid few with unambiguous density and something that is holding them in place, a functional reason should be sought. The expectation is a few outliers, not zero.

MolProbity: More and better reference data for improved all-atom structure validation

This paper describes the current update on macromolecular model validation services that are provided at the MolProbity website, emphasizing changes and additions since the previous review in 2010. There have been many infrastructure improvements, including rewrite of previous Java utilities to now use existing or newly written Python utilities in the open-source CCTBX portion of the Phenix software system. This improves long-term maintainability and enhances the thorough integration of MolProbity-style validation within Phenix. There is now a complete MolProbity mirror site at http://molprobity.manchester.ac.uk. GitHub serves our open-source code, reference datasets, and the resulting multi-dimensional distributions that define most validation criteria. Coordinate output after Asn/Gln/His "flip" correction is now more idealized, since the post-refinement step has apparently often been skipped in the past. Two distinct sets of heavy-atom-to-hydrogen distances and accompanying van der Waals radii have been researched and improved in accuracy, one for the electron-cloud-center positions suitable for X-ray crystallography and one for nuclear positions. New validations include messages at input about problem-causing format irregularities, updates of Ramachandran and rotamer criteria from the million quality-filtered residues in a new reference dataset, the CaBLAM Cα-CO virtual-angle analysis of backbone and secondary structure for cryoEM or low-resolution X-ray, and flagging of the very rare cis-nonProline and twisted peptides which have recently been greatly overused. Due to wide application of MolProbity validation and corrections by the research community, in Phenix, and at the worldwide Protein Data Bank, newly deposited structures have continued to improve greatly as measured by MolProbity's unique all-atom clashscore.

Dissection of Factors Affecting the Variability of the Peptide Bond Geometry and Planarity

Proteins frequently assume complex three-dimensional structures characterized by marginal thermodynamic stabilities. In this scenario, deciphering the folding code of these molecular giants with clay feet is a cumbersome task. Studies performed in last years have shown that the interplay between backbone geometry and local conformation has an important impact on protein structures. Although the variability of several geometrical parameters of protein backbone has been established, the role of the structural context in determining these effects has been hitherto limited to the valence bond angle τ (NC^αC). We here investigated the impact of different factors on the observed variability of backbone geometry and peptide bond planarity. These analyses corroborate the notion that the local conformation expressed in terms of (ϕ, ψ) dihedrals plays a predominant role in dictating the variability of these parameters. The impact of secondary structure is limited to bond angles which involve atoms that are usually engaged in H-bonds and, therefore, more susceptible to the structural context. Present data also show that the nature of the side chain has a significant impact on angles such as NC^αC^β and C^βC^αC. In conclusion, our analyses strongly support the use of variability of protein backbone geometry in structure refinement, validation, and prediction.

Structures and Mechanisms of the Non-Heme Fe(II)- and 2-Oxoglutarate-Dependent Ethylene-Forming Enzyme: Substrate Binding Creates a Twist

The ethylene-forming enzyme (EFE) from Pseudomonas syringae pv. phaseolicola PK2 is a member of the mononuclear nonheme Fe(II)- and 2-oxoglutarate (2OG)-dependent oxygenase superfamily. EFE converts 2OG into ethylene plus three CO2 molecules while also catalyzing the C5 hydroxylation of l-arginine (l-Arg) driven by the oxidative decarboxylation of 2OG to form succinate and CO2. Here we report 11 X-ray crystal structures of EFE that provide insight into the mechanisms of these two reactions. Binding of 2OG in the absence of l-Arg resulted in predominantly monodentate metal coordination, distinct from the typical bidentate metal-binding species observed in other family members. Subsequent addition of l-Arg resulted in compression of the active site, a conformational change of the carboxylate side chain metal ligand to allow for hydrogen bonding with the substrate, and creation of a twisted peptide bond involving this carboxylate and the following tyrosine residue. A reconfiguration of 2OG achieves bidentate metal coordination. The dioxygen binding site is located on the metal face opposite to that facing l-Arg, thus requiring reorientation of the generated ferryl species to catalyze l-Arg hydroxylation. Notably, a phenylalanyl side chain pointing toward the metal may hinder such a ferryl flip and promote ethylene formation. Extensive site-directed mutagenesis studies supported the importance of this phenylalanine and confirmed the essential residues used for substrate binding and catalysis. The structural and functional characterization described here suggests that conversion of 2OG to ethylene, atypical among Fe(II)/2OG oxygenases, is facilitated by the binding of l-Arg which leads to an altered positioning of the carboxylate metal ligand, a resulting twisted peptide bond, and the off-line geometry for dioxygen coordination.

Factors affecting the amplitude of the τ angle in proteins: a revisitation

The protein folded state is the result of the fine balance of a variety of different forces. Even minor structural perturbations may have a significant impact on the stability of these macromolecules. Studies carried out in recent decades have led to the convergent view that proteins are endowed with a flexible spine. One of the open issues related to protein local backbone geometry is the identification of the factors that influence the amplitude of the τ (N—Cα—C) angle. Here, statistical analyses performed on an updated ensemble of X-ray protein structures by dissecting the contribution of the major factors that can potentially influence the local backbone geometry of proteins are reported. The data clearly indicate that the local backbone conformation has a prominent impact on the modulation of the τ angle. Therefore, a proper assessment of the impact of the other potential factors can only be appropriately evaluated when small (φ, ψ) regions are considered. Here, it is shown that when the contribution of the backbone conformation is removed by considering small (φ, ψ) areas, an impact of secondary structure, as defined byDSSP, and/or the residue type on τ is still detectable, although to a limited extent. Indeed, distinct τ-value distributions are detected for Pro/Gly and β-branched (Ile/Val) residues. The key role of the local backbone conformation highlighted here supports the use of variable local backbone geometry in protein refinement protocols.

The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design

Over the past decade, the Rosetta biomolecular modeling suite has informed diverse biological questions and engineering challenges ranging from interpretation of low-resolution structural data to design of nanomaterials, protein therapeutics, and vaccines. Central to Rosetta's success is the energy function: a model parametrized from small-molecule and X-ray crystal structure data used to approximate the energy associated with each biomolecule conformation. This paper describes the mathematical models and physical concepts that underlie the latest Rosetta energy function, called the Rosetta Energy Function 2015 (REF15). Applying these concepts, we explain how to use Rosetta energies to identify and analyze the features of biomolecular models. Finally, we discuss the latest advances in the energy function that extend its capabilities from soluble proteins to also include membrane proteins, peptides containing noncanonical amino acids, small molecules, carbohydrates, nucleic acids, and other macromolecules.

The Dynameomics Entropy Dictionary: A Large-Scale Assessment of Conformational Entropy across Protein Fold Space

Molecular dynamics (MD) simulations contain considerable information with regard to the motions and fluctuations of a protein, the magnitude of which can be used to estimate conformational entropy. Here we survey conformational entropy across protein fold space using the Dynameomics database, which represents the largest existing data set of protein MD simulations for representatives of essentially all known protein folds. We provide an overview of MD-derived entropies accounting for all possible degrees of dihedral freedom on an unprecedented scale. Although different side chains might be expected to impose varying restrictions on the conformational space that the backbone can sample, we found that the backbone entropy and side chain size are not strictly coupled. An outcome of these analyses is the Dynameomics Entropy Dictionary, the contents of which have been compared with entropies derived by other theoretical approaches and experiment. As might be expected, the conformational entropies scale linearly with the number of residues, demonstrating that conformational entropy is an extensive property of proteins. The calculated conformational entropies of folding agree well with previous estimates. Detailed analysis of specific cases identifies deviations in conformational entropy from the average values that highlight how conformational entropy varies with sequence, secondary structure, and tertiary fold. Notably, α-helices have lower entropy on average than do β-sheets, and both are lower than coil regions.

Far-infrared amide IV-VI spectroscopy of isolated 2- and 4-Methylacetanilide

Delocalized molecular vibrations in the far-infrared and THz ranges are highly sensitive to the molecular structure, as well as to intra- and inter-molecular interactions. Thus, spectroscopic studies of biomolecular structures can greatly benefit from an extension of the conventional mid-infrared to the far-infrared wavelength range. In this work, the conformer-specific gas-phase far-infrared spectra of two aromatic molecules containing the peptide -CO-NH- link, namely, 2- and 4-Methylacetanilide, are investigated. The planar conformations with trans configuration of the peptide link have only been observed in the supersonic-jet expansion. The corresponding far-infrared signatures associated with the vibrations of the peptide -CO-NH- moiety, the so-called amide IV-VI bands, have been assigned and compared with the results of density functional theory frequency calculations based on the anharmonic vibrational second-order perturbation theory approach. The analysis of the experimental and theoretical data shows that the amide IV-VI bands are highly diagnostic for the geometry of the peptide moiety and the molecular backbone. They are also strongly blue-shifted upon formation of the NH⋯O-C hydrogen bonding, which is, for example, responsible for the formation of secondary protein structures. Furthermore, the amide IV-VI bands are also diagnostic for the cis configuration of the peptide link, which can be present in cyclic peptides. The experimental gas-phase data presented in this work can assist the vibrational assignment of similar biologically important systems, either isolated or in natural environments.

Charge-density analysis of an iron-sulfur protein at an ultra-high resolution of 0.48 Å

The fine structures of proteins, such as the positions of hydrogen atoms, distributions of valence electrons and orientations of bound waters, are critical factors for determining the dynamic and chemical properties of proteins. Such information cannot be obtained by conventional protein X-ray analyses at 3.0-1.5 Å resolution, in which amino acids are fitted into atomically unresolved electron-density maps and refinement calculations are performed under strong restraints. Therefore, we usually supplement the information on hydrogen atoms and valence electrons in proteins with pre-existing common knowledge obtained by chemistry in small molecules. However, even now, computational calculation of such information with quantum chemistry also tends to be difficult, especially for polynuclear metalloproteins. Here we report a charge-density analysis of the high-potential iron-sulfur protein from the thermophilic purple bacterium Thermochromatium tepidum using X-ray data at an ultra-high resolution of 0.48 Å. Residual electron densities in the conventional refinement are assigned as valence electrons in the multipolar refinement. Iron 3d and sulfur 3p electron densities of the Fe4S4 cluster are visualized around the atoms. Such information provides the most detailed view of the valence electrons of the metal complex in the protein. The asymmetry of the iron-sulfur cluster and the protein environment suggests the structural basis of charge storing on electron transfer. Our charge-density analysis reveals many fine features around the metal complex for the first time, and will enable further theoretical and experimental studies of metalloproteins.

On the reliability of peptide nonplanarity seen in ultra-high resolution crystal structures

Ultra-high resolution protein crystal structures have been considered as relatively reliable sources for defining details of protein geometry, such as the extent to which the peptide unit deviates from planarity. Chellapa and Rose (Proteins 2015; 83:1687) recently called this into question, reporting that for a dozen representative protein structures determined at ∼ 1 Å resolution, the diffraction data could be equally well fit with models restrained to have highly planar peptides, i.e. having a standard deviation of the ω torsion angles of only ∼ 1° instead of the typically observed value of ∼ 6°. Here, we document both conceptual and practical shortcomings of that study and show that the more tightly restrained models are demonstrably incorrect and do not fit the diffraction data equally well. We emphasize the importance of inspecting electron density maps when investigating the agreement between a model and its experimental data. Overall, this report reinforces that modern standard refinement protocols have been well-conceived and that ultra-high resolution protein crystal structures, when evaluated carefully and used with an awareness of their levels of coordinate uncertainty, are powerful sources of information for providing reliable information about the details of protein geometry.

Crystal Structure of an Ammonia-Permeable Aquaporin

Aquaporins of the TIP subfamily (Tonoplast Intrinsic Proteins) have been suggested to facilitate permeation of water and ammonia across the vacuolar membrane of plants, allowing the vacuole to efficiently sequester ammonium ions and counteract cytosolic fluctuations of ammonia. Here, we report the structure determined at 1.18 Å resolution from twinned crystals of Arabidopsis thaliana aquaporin AtTIP2;1 and confirm water and ammonia permeability of the purified protein reconstituted in proteoliposomes as further substantiated by molecular dynamics simulations. The structure of AtTIP2;1 reveals an extended selectivity filter with the conserved arginine of the filter adopting a unique unpredicted position. The relatively wide pore and the polar nature of the selectivity filter clarify the ammonia permeability. By mutational studies, we show that the identified determinants in the extended selectivity filter region are sufficient to convert a strictly water-specific human aquaporin into an AtTIP2;1-like ammonia channel. A flexible histidine and a novel water-filled side pore are speculated to deprotonate ammonium ions, thereby possibly increasing permeation of ammonia. The molecular understanding of how aquaporins facilitate ammonia flux across membranes could potentially be used to modulate ammonia losses over the plasma membrane to the atmosphere, e.g., during photorespiration, and thereby to modify the nitrogen use efficiency of plants.

The structure of an ammonia channel from plants extends our understanding of substrate specificity in different types of aquaporins and reveals an intriguing side pore that raises new questions.

Ammonia is a central molecule in nitrogen metabolism. Aquaporins are integral membrane proteins that form channels that accelerate the passive permeation of small polar uncharged molecules, like water and ammonia, across lipid membranes of the cell. Structural information of ammonia-permeable aquaporins has been lacking. Here, we report a high-resolution structure of the ammonia-permeable aquaporin AtTIP2;1 and explore it by functional assays of mutants and by molecular dynamics simulations. Our data uncover unexpected features of the substrate selectivity filter, including a conserved arginine in a new orientation that is stabilized by interactions to a histidine that is linked to ammonia specificity. An additional histidine in a different part of AtTIP2;1 fortifies the position of the arginine and interacts directly with the substrate in the channel. This histidine is therefore included in an extended selectivity filter, which should prompt a reinterpretation of the determinants of specificity in all types of aquaporins. We speculate that an intriguing water-filled side pore, next to the substrate-binding histidine, participates in deprotonating ammonium ions, which could increase the net permeation of ammonia. Understanding the principles of ammonia permeability may, in the future, allow us to modulate the passage of ammonia and generate crops with higher nitrogen-use efficiency.

How to tackle protein structural data from solution and solid state: An integrated approach

Long-range NMR restraints, such as diamagnetic residual dipolar couplings and paramagnetic data, can be used to determine 3D structures of macromolecules. They are also used to monitor, and potentially to improve, the accuracy of a macromolecular structure in solution by validating or "correcting" a crystal model. Since crystal structures suffer from crystal packing forces they may not be accurate models for the macromolecular structures in solution. However, the presence of real differences should be tested for by simultaneous refinement of the structure using both crystal and solution NMR data. To achieve this, the program REFMAC5 from CCP4 was modified to allow the simultaneous use of X-ray crystallographic and paramagnetic NMR data and/or diamagnetic residual dipolar couplings. Inconsistencies between crystal structures and solution NMR data, if any, may be due either to structural rearrangements occurring on passing from the solution to solid state, or to a greater degree of conformational heterogeneity in solution with respect to the crystal. In the case of multidomain proteins, paramagnetic restraints can provide the correct mutual orientations and positions of domains in solution, as well as information on the conformational variability experienced by the macromolecule.

De novo protein conformational sampling using a probabilistic graphical model

Efficient exploration of protein conformational space remains challenging especially for large proteins when assembling discretized structural fragments extracted from a protein structure data database. We propose a fragment-free probabilistic graphical model, FUSION, for conformational sampling in continuous space and assess its accuracy using ‘blind’ protein targets with a length up to 250 residues from the CASP11 structure prediction exercise. The method reduces sampling bottlenecks, exhibits strong convergence, and demonstrates better performance than the popular fragment assembly method, ROSETTA, on relatively larger proteins with a length of more than 150 residues in our benchmark set. FUSION is freely available through a web server at http://protein.rnet.missouri.edu/FUSION/.

Native proteins trap high-energy transit conformations

During protein folding and as part of some conformational changes that regulate protein function, the polypeptide chain must traverse high-energy barriers that separate the commonly adopted low-energy conformations. How distortions in peptide geometry allow these barrier-crossing transitions is a fundamental open question. One such important transition involves the movement of a non-glycine residue between the left side of the Ramachandran plot (that is, ϕ < 0°) and the right side (that is, ϕ > 0°). We report that high-energy conformations with ϕ ~ 0°, normally expected to occur only as fleeting transition states, are stably trapped in certain highly resolved native protein structures and that an analysis of these residues provides a detailed, experimentally derived map of the bond angle distortions taking place along the transition path. This unanticipated information lays to rest any uncertainty about whether such transitions are possible and how they occur, and in doing so lays a firm foundation for theoretical studies to better understand the transitions between basins that have been little studied but are integrally involved in protein folding and function. Also, the context of one such residue shows that even a designed highly stable protein can harbor substantial unfavorable interactions.

Restricting the ψ Torsion Angle Has Stereoelectronic Consequences on a Scissile Bond: An Electronic Structure Analysis

Protein motion is intimately linked to enzymatic catalysis, yet the stereoelectronic changes that accompany different conformational states of a substrate are poorly defined. Here we investigate the relationship between conformation and stereoelectronic effects of a scissile amide bond. Structural studies have revealed that the C-terminal glycine of ubiquitin and ubiquitin-like proteins adopts a syn (ψ ∼ 0°) or gauche (ψ ∼ ±60°) conformation upon interacting with deubiquitinases/ubiquitin-like proteases. We used hybrid density functional theory and natural bond orbital analysis to understand how the stereoelectronic effects of the scissile bond change as a function of φ and ψ torsion angles. This led to the discovery that when ψ is between 30° and -30° the scissile bond becomes geometrically and electronically deformed. Geometric distortion occurs through pyramidalization of the carbonyl carbon and amide nitrogen. Electronic distortion is manifested by a decrease in the strength of the donor-acceptor interaction between the amide nitrogen and antibonding orbital (π*) of the carbonyl. Concomitant with the reduction in nN → π* delocalization energy, the sp(2) hybrid orbital of the carbonyl carbon becomes richer in p-character, suggesting the syn configuration causes the carbonyl carbon hybrid orbitals to adopt a geometry reminiscent of a tetrahedral-like intermediate. Our work reveals important insights into the role of substrate conformation in activating the reactive carbonyl of a scissile bond. These findings have implications for designing potent active site inhibitors based on the concept of transition state analogues.

Detection of trans-cis flips and peptide-plane flips in protein structures

A coordinate-based method is presented to detect peptide bonds that need correction either by a peptide-plane flip or by a trans-cis inversion of the peptide bond. When applied to the whole Protein Data Bank, the method predicts 4617 trans-cis flips and many thousands of hitherto unknown peptide-plane flips. A few examples are highlighted for which a correction of the peptide-plane geometry leads to a correction of the understanding of the structure-function relation. All data, including 1088 manually validated cases, are freely available and the method is available from a web server, a web-service interface and through WHAT_CHECK.

On interpretation of protein X-ray structures: Planarity of the peptide unit

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 (C-N) 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.

Protein Thermostability Is Owing to Their Preferences to Non-Polar Smaller Volume Amino Acids, Variations in Residual Physico-Chemical Properties and More Salt-Bridges

Introduction

Protein thermostability is an important field for its evolutionary perspective of mesophilic versus thermophilic relationship and for its industrial/ therapeutic applications.

Methods

Presently, a total 400 (200 thermophilic and 200 mesophilic homologue) proteins were studied utilizing several software/databases to evaluate their amino acid preferences. Randomly selected 50 homologous proteins with available PDB-structure of each group were explored for the understanding of the protein charges, isoelectric-points, hydrophilicity, hydrophobicity, tyrosine phosphorylation and salt-bridge occurrences. These 100 proteins were further probed to generate Ramachandran plot/data for the gross secondary structure prediction in and comparison between the thermophilic and mesophilic proteins.

Results

Present results strongly suggest that nonpolar smaller volume amino acids Ala (χ² = 238.54, p<0.001) and Gly (χ² = 73.35, p<0.001) are highly and Val moderately (χ² = 144.43, p<0.001) occurring in the 85% of thermophilic proteins. Phospho-regulated Tyr and redox-sensitive Cys are also moderately distributed (χ²~20.0, p<0.01) in a larger number of thermophilic proteins. A consistent lower distribution of thermophilicity and discretely higher distribution of hydrophobicity is noticed in a large number of thermophilic versus their mesophilic protein homolog. The mean differences of isoelectric points and charges are found to be significantly less (7.11 vs. 6.39, p<0.05 and 1 vs. -0.6, p<0.01, respectively) in thermophilic proteins compared to their mesophilic counterpart. The possible sites for Tyr phosphorylation are noticed to be 25% higher (p<0.05) in thermophilic proteins. The 60% thermophiles are found with higher number of salt bridges in this study. The average percentage of salt-bridge of thermophiles is found to be higher by 20% than their mesophilic homologue. The GLU-HIS and GLU-LYS salt-bridge dyads are calculated to be significantly higher (p<0.05 and p<0.001, respectively) in thermophilic and GLU-ARG is higher in the mesophilic proteins. The Ramachandran plot/ data suggest a higher abundance of the helix, left-handed helix, sheet, nonplanar peptide and lower occurrence of cis peptide, loop/ turn and outlier in thermophiles. Pearson’s correlation result suggests that the isoelectric points of mesophilic and thermophilic proteins are positively correlated (r = 0.93 and 0.84, respectively; p<0.001) to their corresponding charges. And their hydrophilicity is negatively associated with the corresponding hydrophobicity (r = -0.493, p<0.001 and r = -0.324, p<0.05) suggesting their reciprocal evolvement.

Conclusions

Present results for the first time with this large amount of datasets and multiple contributing factors suggest the greater occurrence of hydrophobicity, salt-bridges and smaller volume nonpolar residues (Gly, Ala and Val) and lesser occurrence of bulky polar residues in the thermophilic proteins. A more stoichiometric relationship amongst these factors minimized the hindrance due to side chain burial and increased compactness and secondary structural stability in thermophilic proteins.

Conformational behavior of polyalanine peptides with and without protecting groups of varying chain lengths: population of PP-II structure!

Oculopharyngeal muscular dystrophy (OPMD), a polyalanine myopathy, occurs due to expansion of homo-polyalanine stretch in normal polyadenylating binding protein nuclear 1 (PABPN1) protein from Ala10 to Ala11-17. Therefore, the conformational behavior of polyalanine peptides with n = 10-17, with and without terminal protecting groups, have been investigated with different starting geometries in water by molecular dynamics simulation studies. Alanine peptides are shown to give rise to unordered structure irrespective of starting geometry and not more than two residues at a stretch have the same/similar set of φ, ψ values. However, the final structure with terminal protecting groups look like β-strand. Unprotected poly-Ala peptides adopt twisted β-hairpin/multi hairpin like structure with increasing chain length. The number of residues having φ, ψ values in collagen region is found to be less in peptides with unprotected termini as compared to peptides with protected termini of same chain length. The results have been supported by recent synchrotron radiation circular dichroism spectroscopy of polyproline II and unordered secondary structures. Opening of the helical structure in poly-Ala peptides with protecting groups has been shown to take place from C-terminal and in peptides without protecting groups opening of helix starts from both terminals. Further, opening of helix takes more time in poly-Ala peptides without terminal protecting groups. The deviations in amide bond planarity have been discussed and compared with available experimental and computational results.

High accuracy of Karplus equations for relating three-bond J couplings to protein backbone torsion angles

(3) JC'C' and (3) JHNHα couplings are related to the intervening backbone torsion angle ${\varphi }$ by standard Karplus equations. Although these couplings are known to be affected by parameters other than ${\varphi }$, including H-bonding, valence angles and residue type, experimental results and quantum calculations indicate that the impact of these latter parameters is typically very small. The solution NMR structure of protein GB3, newly refined by using extensive sets of residual dipolar couplings, yields 50-60 % better Karplus equation agreement between ${\varphi }$ angles and experimental (3) JC'C' and (3) JHNHα values than does the high-resolution X-ray structure. In intrinsically disordered proteins, (3) JC'C' and (3) JHNHα couplings can be measured at even higher accuracy, and the impact of factors other than the intervening torsion angle on (3) J will be smaller than in folded proteins, making these couplings exceptionally valuable reporters on the ensemble of ${\varphi }$ angles sampled by each residue.

Blind prediction performance of RosettaAntibody 3.0: grafting, relaxation, kinematic loop modeling, and full CDR optimization

Antibody Modeling Assessment II (AMA-II) provided an opportunity to benchmark RosettaAntibody on a set of 11 unpublished antibody structures. RosettaAntibody produced accurate, physically realistic models, with all framework regions and 42 of the 55 non-H3 CDR loops predicted to under an Ångström. The performance is notable when modeling H3 on a homology framework, where RosettaAntibody produced the best model among all participants for four of the 11 targets, two of which were predicted with sub-Ångström accuracy. To improve RosettaAntibody, we pursued the causes of model errors. The most common limitation was template unavailability, underscoring the need for more antibody structures and/or better de novo loop methods. In some cases, better templates could have been found by considering residues outside of the CDRs. De novo CDR H3 modeling remains challenging at long loop lengths, but constraining the C-terminal end of H3 to a kinked conformation allows near-native conformations to be sampled more frequently. We also found that incorrect VL -VH orientations caused models with low H3 RMSDs to score poorly, suggesting that correct VL -VH orientations will improve discrimination between near-native and incorrect conformations. These observations will guide the future development of RosettaAntibody.

Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement

Ideal values of bond angles and lengths used as external restraints are crucial for the successful refinement of protein crystal structures at all but the highest of resolutions. The restraints in common use today have been designed on the assumption that each type of bond or angle has a single ideal value that is independent of context. However, recent work has shown that the ideal values are, in fact, sensitive to local conformation, and, as a first step towards using such information to build more accurate models, ultra-high-resolution protein crystal structures have been used to derive a conformation-dependent library (CDL) of restraints for the protein backbone [Berkholz et al. (2009) Structure 17, 1316-1325]. Here, we report the introduction of this CDL into the phenix package and the results of test refinements of thousands of structures across a wide range of resolutions. These tests show that use of the CDL yields models that have substantially better agreement with ideal main-chain bond angles and lengths and, on average, a slightly enhanced fit to the X-ray data. No disadvantages of using the backbone CDL are apparent. In phenix, use of the CDL can be selected by simply specifying the cdl = True option. This successful implementation paves the way for further aspects of the context dependence of ideal geometry to be characterized and applied to improve experimental and predictive modeling accuracy.

An Anisotropic Coarse-Grained Model for Proteins Based On Gay-Berne and Electric Multipole Potentials

Gay–Berne anisotropic potential has been widely used to evaluate the nonbonded interactions between coarse-grained particles being described as elliptical rigid bodies. In this paper, we are presenting a coarse-grained model for twenty kinds of amino acids and proteins, based on the anisotropic Gay–Berne and point electric multipole (EMP) potentials. We demonstrate that the anisotropic coarse-grained model, namely GBEMP model, is able to reproduce many key features observed from experimental protein structures (Dunbrack Library), as well as from atomistic force field simulations (using AMOEBA, AMBER, and CHARMM force fields), while saving the computational cost by a factor of about 10–200 depending on specific cases and atomistic models. More importantly, unlike other coarse-grained approaches, our framework is based on the fundamental intermolecular forces with explicit treatment of electrostatic and repulsion-dispersion forces. As a result, the coarse-grained protein model presented an accurate description of nonbonded interactions (particularly electrostatic component) between hetero/homodimers (such as peptide–peptide, peptide–water). In addition, the encouraging performance of the model was reflected by the excellent correlation between GBEMP and AMOEBA models in the calculations of the dipole moment of peptides. In brief, the GBEMP model given here is general and transferable, suitable for simulating complex biomolecular systems.

Interplay between peptide bond geometrical parameters in nonglobular structural contexts

Several investigations performed in the last two decades have unveiled that geometrical parameters of protein backbone show a remarkable variability. Although these studies have provided interesting insights into one of the basic aspects of protein structure, they have been conducted on globular and water-soluble proteins. We report here a detailed analysis of backbone geometrical parameters in nonglobular proteins/peptides. We considered membrane proteins and two distinct fibrous systems (amyloid-forming and collagen-like peptides). Present data show that in these systems the local conformation plays a major role in dictating the amplitude of the bond angle N-C(α)-C and the propensity of the peptide bond to adopt planar/nonplanar states. Since the trends detected here are in line with the concept of the mutual influence of local geometry and conformation previously established for globular and water-soluble proteins, our analysis demonstrates that the interplay of backbone geometrical parameters is an intrinsic and general property of protein/peptide structures that is preserved also in nonglobular contexts. For amyloid-forming peptides significant distortions of the N-C(α)-C bond angle, indicative of sterical hidden strain, may occur in correspondence with side chain interdigitation. The correlation between the dihedral angles Δω/ψ in collagen-like models may have interesting implications for triple helix stability.

Improvements to robotics-inspired conformational sampling in rosetta

To accurately predict protein conformations in atomic detail, a computational method must be capable of sampling models sufficiently close to the native structure. All-atom sampling is difficult because of the vast number of possible conformations and extremely rugged energy landscapes. Here, we test three sampling strategies to address these difficulties: conformational diversification, intensification of torsion and omega-angle sampling and parameter annealing. We evaluate these strategies in the context of the robotics-based kinematic closure (KIC) method for local conformational sampling in Rosetta on an established benchmark set of 45 12-residue protein segments without regular secondary structure. We quantify performance as the fraction of sub-Angstrom models generated. While improvements with individual strategies are only modest, the combination of intensification and annealing strategies into a new “next-generation KIC” method yields a four-fold increase over standard KIC in the median percentage of sub-Angstrom models across the dataset. Such improvements enable progress on more difficult problems, as demonstrated on longer segments, several of which could not be accurately remodeled with previous methods. Given its improved sampling capability, next-generation KIC should allow advances in other applications such as local conformational remodeling of multiple segments simultaneously, flexible backbone sequence design, and development of more accurate energy functions.

Energetically unfavorable amide conformations for N6-acetyllysine side chains in refined protein structures

The reversible acetylation of lysine to form N6-acetyllysine in the regulation of protein function is a hallmark of epigenetics. Acetylation of the positively charged amino group of the lysine side chain generates a neutral N-alkylacetamide moiety that serves as a molecular "switch" for the modulation of protein function and protein-protein interactions. We now report the analysis of 381 N6-acetyllysine side chain amide conformations as found in 79 protein crystal structures and 11 protein NMR structures deposited in the Protein Data Bank (PDB) of the Research Collaboratory for Structural Bioinformatics. We find that only 74.3% of N6-acetyllysine residues in protein crystal structures and 46.5% in protein NMR structures contain amide groups with energetically preferred trans or generously trans conformations. Surprisingly, 17.6% of N6-acetyllysine residues in protein crystal structures and 5.3% in protein NMR structures contain amide groups with energetically unfavorable cis or generously cis conformations. Even more surprisingly, 8.1% of N6-acetyllysine residues in protein crystal structures and 48.2% in NMR structures contain amide groups with energetically prohibitive twisted conformations that approach the transition state structure for cis-trans isomerization. In contrast, 109 unique N-alkylacetamide groups contained in 84 highly accurate small molecule crystal structures retrieved from the Cambridge Structural Database exclusively adopt energetically preferred trans conformations. Therefore, we conclude that cis and twisted N6-acetyllysine amides in protein structures deposited in the PDB are erroneously modeled due to their energetically unfavorable or prohibitive conformations.

Functional modulation of a protein folding landscape via side-chain distortion

Ultrahigh-resolution (< 1.0 Å) structures have revealed unprecedented and unexpected details of molecular geometry, such as the deformation of aromatic rings from planarity. However, the functional utility of such energetically costly strain is unknown. The 0.83 Å structure of α-lytic protease (αLP) indicated that residues surrounding a conserved Phe side-chain dictate a rotamer which results in a ~6° distortion along the side-chain, estimated to cost 4 kcal/mol. By contrast, in the closely related protease Streptomyces griseus Protease B (SGPB), the equivalent Phe adopts a different rotamer and is undistorted. Here, we report that the αLP Phe side-chain distortion is both functional and conserved in proteases with large pro regions. Sequence analysis of the αLP serine protease family reveals a bifurcation separating those sequences expected to induce distortion and those that would not, which correlates with the extent of kinetic stability. Structural and folding kinetics analyses of family members suggest that distortion of this side-chain plays a role in increasing kinetic stability within the αLP family members that use a large Pro region. Additionally, structural and kinetic folding studies of mutants demonstrate that strain alters the folding free energy landscape by destabilizing the transition state (TS) relative to the native state (N). Although side-chain distortion comes at a cost of foldability, it suppresses the rate of unfolding, thereby enhancing kinetic stability and increasing protein longevity under harsh extracellular conditions. This ability of a structural distortion to enhance function is unlikely to be unique to αLP family members and may be relevant in other proteins exhibiting side-chain distortions.