Error estimates in atom coordinates and B factors in macromolecular crystallography

The overall diffraction precision index (DPI) of a biological macromolecule crystal structure was first described by Cruickshank in 1999. This topical review proceeds from this point and describes the subsequent elaboration of the index to individual atom coordinates. Additional developments were introduced by the availability of a webserver, which provides a transformed PDB entry with individual atom coordinate errors derived from applying the DPI method using the parameters provided by the authors and then subsequently added to the PDB file. This webserver has been extensively used and harnessed in describing non-covalent distance error estimates as well as assessing the significance, or otherwise, of atom movements in a variety of studies. The standard uncertainties on a biological macromolecule's atomic displacement parameters (the 'B factors') has been an entirely different challenge but is obviously important since the crystallographic community has developed the habit of quoting B factors to a false precision in papers. This can convey a false certainty in the dynamics of a structure. A method involving parallelisation of workflows for diffraction image data processing does however offer estimates of the precision of B factors.

Observations on Laue diffraction within synchrotron radiation and neutron macromolecular crystallography research and developments

A seminal contribution in the domain of physiologically relevant biological structure and function determination was by Keith Moffat, of Cornell and latterly of the University of Chicago proposing that synchrotrons should offer the option of a Laue method data collection mode. I enthusiastically joined in supporting this initiative. This proposal needed detailed methods development though; theoretical, experimental and software development. This work was added to the broad research and development program of synchrotron radiation at the UK's SRS. This whole program led to knowledge transfer from the UK's SRS to the ESRF as well as for neutron Laue protein crystallography to the reactor spallation sources and later to spallation neutron sources.

Combining temperature perturbations with X-ray crystallography to study dynamic macromolecules: A thorough discussion of experimental methods

Temperature is an important state variable that governs the behavior of microscopic systems, yet crystallographers rarely exploit temperature changes to study the structure and dynamics of biological macromolecules. In fact, approximately 90% of crystal structures in the Protein Data Bank were determined under cryogenic conditions, because sample cryocooling makes crystals robust to X-ray radiation damage and facilitates data collection. On the other hand, cryocooling can introduce artifacts into macromolecular structures, and can suppress conformational dynamics that are critical for function. Fortunately, recent advances in X-ray detector technology, X-ray sources, and computational data processing algorithms make non-cryogenic X-ray crystallography easier and more broadly applicable than ever before. Without the reliance on cryocooling, high-resolution crystallography can be combined with various temperature perturbations to gain deep insight into the conformational landscapes of macromolecules. This Chapter reviews the historical reasons for the prevalence of cryocooling in macromolecular crystallography, and discusses its potential drawbacks. Next, the Chapter summarizes technological developments and methodologies that facilitate non-cryogenic crystallography experiments. Finally, the chapter discusses the theoretical underpinnings and practical aspects of multi-temperature and temperature-jump crystallography experiments, which are powerful tools for understanding the relationship between the structure, dynamics, and function of proteins and other biological macromolecules.

Relating protein crystal structure to ligand-binding thermodynamics

An important interface between biophysical chemistry and biological crystal structures involves whether it is possible to relate experimental calorimetry measurements of protein ligand binding to 3D structures. This has proved to be challenging. The probes of the structure of matter, namely X-rays, neutrons and electrons, have challenges of one type or another in their use. This article focuses on saccharide binding to lectins as a theme, yet after 25 years or so it is still a work in progress to connect 3D structure to binding energies. Whilst this study involved one type of protein (lectins) and one class of ligand (monosaccharides), i.e. it was specific, it was of general importance, as measured for instance by its wide impact. The impetus for writing this update now, as a Scientific Comment, is that a breakthrough in neutron crystal structure determinations of saccharide-bound lectins has been achieved. It is suggested here that this new research from neutron protein crystallography could improve, i.e. reduce, the errors in the estimated binding energies.

Pre- and Post-publication Verification for Reproducible Data Mining in Macromolecular Crystallography

Like an article narrative is deemed by an editor and referees to be worthy of being a version of record on acceptance as a publication, so must the underpinning data also be scrutinized before passing it as a version of record. Indeed without the underpinning data, a study and its conclusions cannot be reproduced at any stage of evaluation, pre- or post-publication. Likewise, an independent study without its own underpinning data also cannot be reproduced let alone be considered a replicate of the first study. The PDB is a modern marvel of achievement providing an organized open access to depositor and user of the data held there opening numerous applications. Methods for modeling protein structures and for determination of structures are still improving their precision, and artifacts of the method exist. So their accuracy is realized if they are reproduced by other methods. It is on such foundations that reproducible data mining is based. Data rates are expanding considerably be they at synchrotrons, the X-ray free electron lasers (XFELs), electron cryomicroscopes (cryoEM), or at the neutron facilities. The work of a person as a referee or user with a narrative and its underpinning data may well be complemented in future by artificial intelligence with machine learning, the former for specific refereeing and the latter for the more general validation, both ideally before publication. Examples are described involving rhenium theranostics, the anti-cancer platins and the SARS-CoV-2 main protease.

Solvent Perturbation of Protein Structures - A Review Study with Lectins

Use of organic molecules as co-solvent with water, the ubiquitous biological solvent, to perturb the structure of proteins is popular in the research area of protein structure and folding. These organic co-solvents are believed to somehow mimic the environment near the cell membrane. Apart from that they induce non-native states which can be present in the protein folding pathway or those states also may be representative of the off pathway structures leading to amyloid formation, responsible for various fatal diseases. In this review, we shall focus on organic co-solvent induced structure perturbation of various members of lectin family. Lectins are excellent model systems for protein folding study because of its wide occurrence, diverse structure and versatile biological functions. Lectins were mainly perturbed by two fluoroalcohols - 2,2,2- trifluoroethanol and 1,1,1,3,3,3-hexafluoroisopropanol whereas glycerol, ethylene glycol and polyethylene glycols were used in some cases. Overall, all native lectins were denatured by alcohols and most of the denatured lectins have predominant helical secondary structure. But characterization of the helical states and the transition pathway for various lectins revealed diverse result.

Fundamentals of neutron crystallography in structural biology

This chapter introduces this topic for the whole volume. It is not a review, rather it presents the basics, the key considerations and forward references to the other chapters. This starts by setting the scene of principles and overall strategy, moves onto planning an experiment including its feasibility and then outlines practicalities with options for the experiment. The crystal structure that results will lead to publication and associated with it, Protein Data Bank deposition.

IMAGINE: The neutron protein crystallography beamline at the high flux isotope reactor

IMAGINE is a high intensity, quasi-Laue neutron crystallography beamline developed at the 85MW High Flux Isotope Reactor (HFIR) at Oak Ridge National Laboratory (ORNL). This state-of-the-art facility for neutron-diffraction enables neutron protein structures to be determined at or near atomic resolutions from crystals with volumes of <1mm³ and unit cell edges of <150Å. The beamline features include elliptical focusing mirrors that deliver neutrons into a 2.0×3.2mm² focal spot at the sample position, and variable short and long wavelength cutoff optics that provide automated exchange between multiple wavelength configurations. The beamline is equipped with a single-axis goniometer, neutron-sensitive cylindrical image plate detector and room temperature and cryogenic sample environments. This article describes the beamline components, the diffractometer and the data collection and data analysis protocols that are used, and outlines the protein deuteration, crystallization and conventional crystallography capabilities that are available to users at ORNL's neutron facilities. We also present examples of the scientific questions being addressed at this beamline and highlight important findings in enzyme chemistry that have been made possible by IMAGINE.

Mannobiose Binding Induces Changes in Hydrogen Bonding and Protonation States of Acidic Residues in Concanavalin A As Revealed by Neutron Crystallography

Plant lectins are carbohydrate-binding proteins with various biomedical applications. Concanavalin A (Con A) holds promise in treating cancerous tumors. To better understand the Con A carbohydrate binding specificity, we obtained a room-temperature neutron structure of this legume lectin in complex with a disaccharide Manα1-2Man, mannobiose. The neutron structure afforded direct visualization of the hydrogen bonding between the protein and ligand, showing that the ligand is able to alter both protonation states and interactions for residues located close to and distant from the binding site. An unprecedented low-barrier hydrogen bond was observed forming between the carboxylic side chains of Asp28 and Glu8, with the D atom positioned equidistant from the oxygen atoms having an O···D···O angle of 101.5°.

The use of small-molecule structures to complement protein-ligand crystal structures in drug discovery

Many ligand-discovery stories tell of the use of structures of protein-ligand complexes, but the contribution of structural chemistry is such a core part of finding and improving ligands that it is often overlooked. More than 800 000 crystal structures are available to the community through the Cambridge Structural Database (CSD). Individually, these structures can be of tremendous value and the collection of crystal structures is even more helpful. This article provides examples of how small-molecule crystal structures have been used to complement those of protein-ligand complexes to address challenges ranging from affinity, selectivity and bioavailability though to solubility.

Novel calcium recognition constructions in proteins: Calcium blade and EF-hand zone

Metal ions can regulate various cell processes being first, second or third messengers, and some of them, especially transition metal ions, take part in catalysis in many enzymes. As an intracellular ion, Ca²⁺ is involved in many cellular functions from fertilization and contraction, cell differentiation and proliferation, to apoptosis and cancer. Here, we have identified and described two novel calcium recognition environments in proteins: the calcium blade zone and the EF-hand zone, common to 12 and 8 different protein families, respectively. Each of the two environments contains three distinct structural elements: (a) the well-known characteristic Dx[DN]xDG motif; (b) an adjacent structurally identical segment, which binds metal ion in the same way between the calcium blade zone and the EF-hand zone; and (c) the following structurally variable segment, which distinguishes the calcium blade zone from the EF-hand zone. Both zones have sequence insertions between the last residue of the zone and calcium-binding residues in positions V or VI. The long insertion often connects the active and the calcium-binding sites in proteins. Using the structurally identical segments as an anchor, we were able to construct the classical calmodulin type EF-hand calcium-binding site out of two different calcium-binding motifs from two unrelated proteins.

Waters in room temperature and cryo protein crystal structures

Since it has been observed that low temperature protein crystal structures may differ from room temperature structures, it is necessary to compare systematically the protein hydration structure in low and room protein crystal structures. High quality data sets of protein structures were built in an extremely rigorous manner and crystal symmetry was included in the identification of four types of water molecules (buried in the protein core, deeply inserted into crevices at the protein surface, first and second hydration layers). More water molecules are observed at low temperature only if the resolution is better than 2.1–2.3 Å. At worse resolution, temperature does not play any role. The numerous water molecules that become detectable at low temperature and at higher resolution are more mobile, relative to the protein average flexibility. Despite that, the occupancy does not depend on temperature. It can be hypothesized that water structure and around proteins and hydrogen bond network do not depend on the temperature, at least in the temperature range examined here. At low temperature more water molecules are detected because the average flexibility of all the atoms decreases, so that also water molecules that are considerably more mobile than the average atoms become observable in the electron density maps.

Assessing Spectral Simulation Protocols for the Amide I Band of Proteins

We present a benchmark study of spectral simulation protocols for the amide I band of proteins. The amide I band is widely used in infrared spectroscopy of proteins due to the large signal intensity, high sensitivity to hydrogen bonding, and secondary structural motifs. This band has, thus, proven valuable in many studies of protein structure-function relationships. We benchmark spectral simulation protocols using two common force fields in combination with several electrostatic mappings and coupling models. The results are validated against experimental linear absorption and two-dimensional infrared spectroscopy for three well-studied proteins. We find two-dimensional infrared spectroscopy to be much more sensitive to the simulation protocol than linear absorption and report on the best simulation protocols. The findings demonstrate that there is still room for ideas to improve the existing models for the amide I band of proteins.

Application of two-dimensional infrared spectroscopy to benchmark models for the amide I band of proteins

In this paper, we present a novel benchmarking method for validating the modelling of vibrational spectra for the amide I region of proteins. We use the linear absorption spectra and two-dimensional infrared spectra of four experimentally well-studied proteins as a reference and test nine combinations of molecular dynamics force fields, vibrational frequency mappings, and coupling models. We find that two-dimensional infrared spectra provide a much stronger test of the models than linear absorption does. The best modelling approach in the present study still leaves significant room for future improvement. The presented benchmarking scheme, thus, provides a way of validating future protocols for modelling the amide I band in proteins.

Introducing DInaMo: A Package for Calculating Protein Circular Dichroism Using Classical Electromagnetic Theory

The dipole interaction model is a classical electromagnetic theory for calculating circular dichroism (CD) resulting from the π-π* transitions of amides. The theoretical model, pioneered by J. Applequist, is assembled into a package, DInaMo, written in Fortran allowing for treatment of proteins. DInaMo reads Protein Data Bank formatted files of structures generated by molecular mechanics or reconstructed secondary structures. Crystal structures cannot be used directly with DInaMo; they either need to be rebuilt with idealized bond angles and lengths, or they need to be energy minimized to adjust bond lengths and bond angles because it is common for crystal structure geometries to have slightly short bond lengths, and DInaMo is sensitive to this. DInaMo reduces all the amide chromophores to points with anisotropic polarizability and all nonchromophoric aliphatic atoms including hydrogens to points with isotropic polarizability; all other atoms are ignored. By determining the interactions among the chromophoric and nonchromophoric parts of the molecule using empirically derived polarizabilities, the rotational and dipole strengths are determined leading to the calculation of CD. Furthermore, ignoring hydrogens bound to methyl groups is initially explored and proves to be a good approximation. Theoretical calculations on 24 proteins agree with experiment showing bands with similar morphology and maxima.

Variations in Mn(II) speciation among organisms: what makes D. radiodurans different

The manganese(II) speciation in intact cells of D. radiodurans, E. coli, S. cerevisiae and Arabidopsis thaliana seeds was measured using high-field electron paramagnetic resonance techniques. The majority of the Mn(II) ions in these organisms were six-coordinate, bound predominately by water, phosphates and nitrogen-based molecules. The relative distribution of the different phosphates in bacteria and S. cerevisiae was the same and dominated by monophosphate monoesters. Mn(II) was also found bound to the phosphate backbone of nucleic acids in these organisms. Phosphate ligation in Arabidopsis seeds was dominated by phytate. The extent of nitrogen ligation in the four organisms was also determined. On average, the Mn(II) in D. radiodurans had the most nitrogen ligands followed by E. coli. This was attributed to higher concentrations of Mn(II) bound to proteins in these species. Although constitutively expressed in all four organisms, MnSOD was only detected in D. radiodurans. As previously reported, D. radiodurans also accumulates a second abundant Mn containing protein species. The high concentration of proteinaceous Mn(II) is a unique feature of D. radiodurans.

Structural studies of an anti-inflammatory lectin from Canavalia boliviana seeds in complex with dimannosides

Plant lectins, especially those purified from species of the Leguminosae family, represent the best-studied group of carbohydrate-binding proteins. Lectins purified from seeds of the Diocleinae subtribe exhibit a high degree of sequence identity notwithstanding that they show very distinct biological activities. Two main factors have been related to this feature: variance in key residues influencing the carbohydrate-binding site geometry and differences in the pH-dependent oligomeric state profile. In this work, we have isolated a lectin from Canavalia boliviana (Cbol) and solved its x-ray crystal structure in the unbound form and in complex with the carbohydrates Man(α1-3)Man(α1-O)Me, Man(α1-4)Man(α1-O)Me and 5-bromo-4-chloro-3-indolyl-α-D-mannose. We evaluated its oligomerization profile at different pH values using Small Angle X-ray Scattering and compared it to that of Concanavalin A. Based on predicted pKa-shifts of amino acids in the subunit interfaces we devised a model for the dimer-tetramer equilibrium phenomena of these proteins. Additionally, we demonstrated Cbol anti-inflammatory properties and further characterized them using in vivo and in vitro models.

Structure and nature of manganese(II) imidazole complexes in frozen aqueous solutions

A common feature of a large majority of the manganese metalloenzymes, as well as many synthetic biomimetic complexes, is the bonding between the manganese ion and imidazoles. This interaction was studied by examining the nature and structure of manganese(II) imidazole complexes in frozen aqueous solutions using 285 GHz high magnet-field continuous-wave electron paramagnetic resonance (cw-HFEPR) and 95 GHz pulsed electron-nuclear double resonance (ENDOR) and pulsed electron-double resonance detected nuclear magnetic resonance (PELDOR-NMR). The (55)Mn hyperfine coupling and isotropic g values of Mn(II) in frozen imidazole solutions continuously decreased with increasing imidazole concentration. ENDOR and PELDOR-NMR measurements demonstrated that the structural basis for this behavior arose from the imidazole concentration-dependent distribution of three six-coordinate and two four-coordinate species: [Mn(H2O)6](2+), [Mn(imidazole)(H2O)5](2+), [Mn(imidazole)2(H2O)4](2+), [Mn(imidazole)3(H2O)](2+), and [Mn(imidazole)4](2+). The hyperfine and g values of manganese proteins were also fully consistent with this imidazole effect. Density functional theory methods were used to calculate the structures, spin and charge densities, and hyperfine couplings of a number of different manganese imidazole complexes. The use of density functional theory with large exact-exchange admixture calculations gave isotropic (55)Mn hyperfine couplings that were semiquantitative and of predictive value. The results show that the covalency of the Mn-N bonds play an important role in determining not only magnetic spin parameters but also the structure of the metal binding site. The relationship between the isotropic (55)Mn hyperfine value and the number of imidazole ligands provides a quick and easy test for determining whether a protein binds an Mn(II) ion using histidine residues and, if so, how many are involved. Application of this method shows that as much as 40% of the Mn(II) ions in Deinococcus radiodurans are ligated to two histidines (Tabares, L. C.; Un, S. J. Biol. Chem 2013, in press).

PowerBorn: A Barnes-Hut Tree Implementation for Accurate and Efficient Born Radii Computation

Implicit solvent models are one of the standard tools in computational biophysics. While Poisson-Boltzmann methods offer highly accurate results within this framework, generalized Born models have been used due to their higher computational efficiency in many (bio)molecular simulations, where computational power is a limiting factor. In recent years, there have been remarkable advances to reduce some deficiencies in the generalized Born models. On the other hand, these advances come at an increased computational cost that contrasts the reasons for choosing generalized Born models over Poisson-Boltzmann methods. To address this performance issue, we present a new algorithm for Born radii computation, one performance critical part in the evaluation of generalized Born models, which is based on a Barnes-Hut tree code scheme. We show that an implementation of this algorithm provides accurate Born radii and polar solvation free energies in comparison to Poisson-Boltzmann computations, while delivering up to an order of magnitude better performance over existing, similarly accurate methods. The C++ implementation of this algorithm will be available at http://www.int.kit.edu/nanosim/ .

Trifluoroethanol-induced conformational change of tetrameric and monomeric soybean agglutinin: role of structural organization and implication for protein folding and stability

2,2,2-Trifuoroethanol (TFE)-induced conformational structure change of a β-sheet legume lectin, soybean agglutinin (SBA) has been investigated employing its exclusive structural forms in quaternary (tetramer) and tertiary (monomer) states, by far- and near-UV CD, FTIR, fluorescence, low temperature phosphorescence and chemical modification. Far-UV CD results show that, for SBA tetramer, native atypical β-conformation transforms to a highly α-helical structure, with the helical content reaching 57% in 95% TFE. For SBA monomer, atypical β-sheet first converts to typical β-sheet at low TFE concentration (10%), which then leads to a nonnative α-helix at higher TFE concentration. From temperature-dependent studies (5-60 °C) of TFE perturbation, typical β-sheet structure appears to be less stable than atypical β-sheet and the induced helix entails reduced thermal stability. The heat induced transitions are reversible except for atypical to typical β-sheet conversion. FTIR results reveal a partial α-helix conversion at high protein concentration but with quantitative yield. However, aggregation is detected with FTIR at lower TFE concentration, which disappears in more TFE. Near-UV CD, fluorescence and phosphorescence studies imply the existence of an intermediate with native-like secondary and tertiary structure, which could be related to the dissociation of tetramer to monomer. This has been further supported by concentration dependent far-UV CD studies. Chemical modification with N-bromosuccinimide (NBS) shows that all six tryptophans per monomer are solvent-exposed in the induced α-helical conformation. These results may provide novel and important insights into the perturbed folding problem of SBA in particular, and β-sheet oligomeric proteins in general.

Spatial distribution of radiation damage to crystalline proteins at 25-300 K

The spatial distribution of radiation damage (assayed by increases in atomic B factors) to thaumatin and urease crystals at temperatures ranging from 25 to 300 K is reported. The nature of the damage changes dramatically at approximately 180 K. Above this temperature the role of solvent diffusion is apparent in thaumatin crystals, as solvent-exposed turns and loops are especially sensitive. In urease, a flap covering the active site is the most sensitive part of the molecule and nearby loops show enhanced sensitivity. Below 180 K sensitivity is correlated with poor local packing, especially in thaumatin. At all temperatures, the component of the damage that is spatially uniform within the unit cell accounts for more than half of the total increase in the atomic B factors and correlates with changes in mosaicity. This component may arise from lattice-level, rather than local, disorder. The effects of primary structure on radiation sensitivity are small compared with those of tertiary structure, local packing, solvent accessibility and crystal contacts.

On the Role of Water Models in Quantifying the Binding Free Energy of Highly Conserved Water Molecules in Proteins: The Case of Concanavalin A

The ability of ligands to displace conserved water molecules in protein binding sites is of significant interest in drug design and is particularly pertinent in the case of glycomimetic drugs. This concept was explored in previous work [ Clarke et al. J. Am. Chem. Soc. 2001 , 123 , 12238 - 12247 and Kadirvelraj et al. J. Am. Chem. Soc. 2008 , 130 , 16933 - 16942 ] for a highly conserved water molecule located in the binding site of the prototypic carbohydrate-binding protein Concanavalin A (Con A). A synthetic ligand was designed with the aim of displacing such water. While the synthetic ligand bound to Con A in an analogous manner to that of the natural ligand, crystallographic analysis demonstrated that it did not displace the conserved water. In order to quantify the affinity of this particular water for the Con A surface, we report here the calculated standard binding free energy for this water in both ligand-bound and free Con A, employing three popular water models: TIP3P, TIP4P, and TIP5P. Although each model was developed to perform well in simulations of bulk-phase water, the computed binding energies for the isolated water molecule displayed a high sensitivity to the model. Both molecular dynamics simulation and free energy results indicate that the choice of water model may greatly influence the characterization of surface water molecules as conserved (TIP5P) or not (TIP3P) in protein binding sites, an observation of considerable significance to rational drug design. Structural and theoretical aspects at the basis of the different behaviors are identified and discussed.

Dark progression reveals slow timescales for radiation damage between T = 180 and 240 K

Can radiation damage to protein crystals be `outrun' by collecting a structural data set before damage is manifested? Recent experiments using ultra-intense pulses from a free-electron laser show that the answer is yes. Here, evidence is presented that significant reductions in global damage at temperatures above 200 K may be possible using conventional X-ray sources and current or soon-to-be available detectors. Specifically, `dark progression' (an increase in damage with time after the X-rays have been turned off) was observed at temperatures between 180 and 240 K and on timescales from 200 to 1200 s. This allowed estimation of the temperature-dependent timescale for damage. The rate of dark progression is consistent with an Arrhenius law with an activation energy of 14 kJ mol(-1). This is comparable to the activation energy for the solvent-coupled diffusive damage processes responsible for the rapid increase in radiation sensitivity as crystals are warmed above the glass transition near 200 K. Analysis suggests that at T = 300 K data-collection times of the order of 1 s (and longer at lower temperatures) may allow significant reductions in global radiation damage, facilitating structure solution on crystals with liquid solvent. No dark progression was observed below T = 180 K, indicating that no important damage process is slowed through this timescale window in this temperature range.

Localization and environment of tryptophans in different structural states of concanavalin A

We have investigated the localization and environment of tryptophan residues in different quaternary and conformational states (tetrameric, dimeric, monomeric and unfolded) of metallized and demetallized concanavalin A (ConA) by selective chemical modification, fluorescence, and phosphorescence. ConA has four tryptophan residues (Trp 40, Trp 88, Trp 109 and Trp 182) per subunit. The pattern of oxidation by N-bromosuccinimide (NBS) shows that NBS modifies, in dimer, only Trp 182 which remains inaccessible in tetramer, two (Trp 88 along with Trp 182) in monomer, all four in unfolded form in presence of EDTA, and three (possibly Trp 40 along with Trp 88 and Trp 182) in unfolded form from native or remetallized ConA. Utilizing wavelength-selective fluorescence approach, we have observed a red edge excitation shift (REES) of 6-8 nm for tetramer and dimer. A more pronounced REES (11 nm) is observed for oxidized monomer compared to REES (3 nm) for unoxidized species. Acrylamide quenching shows the Stern-Volmer constant (K(SV)) for dimer, monomer, unfolded ConA and unfolded apo-ConA being 3.8, 5.2, 12.8, 14.0 M(-1), respectively. Phosphorescence studies at 77 K give more structured spectra, with two (0,0) bands at 406.2 (weak) and 413.2 nm for tetramer. However, a single (0,0) band appears at 413.2 for dimer and 412.6 nm for monomer, while the (0,0) band of the oxidized monomer is red shifted to 414.4 nm. These results may provide important insight into subtlety of organization and environment of tryptophans in the context of folding and structural studies of oligomeric proteins including lectins.

Ligand-induced fit affects binding modes and provokes changes in crystal packing of aldose reductase

BACKGROUND

Flexibility is a common feature of proteins. For human aldose reductase, a variety of conformers have been observed in crystalline complexes with different inhibitors.

METHODS

A study of crystal structures and isothermal titration calorimetry was performed on wild type and mutated aldose reductase.

RESULTS AND CONCLUSIONS

Though the interaction to the mutated residue Thr113 does not directly alter the binding mode of zopolrestat to aldose reductase, a shift of its basic scaffold is induced which affects the interaction with a flexible loop and introduces disorder. With the related inhibitor IDD393, two distinct binding site conformations result in two different crystal forms: While a backbone flip of the same residues as for zopolrestat is present in both crystal forms, a considerable side-chain movement of a phenylalanine is observed for only one crystal form. In consequence, residual mobility of adjacent amino acids is increased and some crystal contacts are prevented which reinforces different crystal packing. The structure of a benzothiazepine reveals a protein conformer, where this phenylalanine is further relocated resulting in the same altered crystal packing. Differences in the thermodynamic signature recorded for the various complexes relate to the structural differences.

GENERAL SIGNIFICANCE

Crystal structures are accepted as "gold standard" for the interpretation of protein geometry, however, they are only one possible structure and can be influenced by crystal packing. In reverse, ligand binding can affect protein conformation and determine crystal packing. The phenomenon of such "polymorphic forms" is well appreciated, however rarely understood at the molecular level.

Photo- and biophysical studies of lectin-conjugated fluorescent nanoparticles: reduced sensitivity in high density assays

Lectin-conjugated, fluorescent silica nanoparticles (fNP) have been developed for carbohydrate-based histopathology evaluations of epithelial tissue biopsies. The fNP platform was selected for its enhanced emissive brightness compared to direct dye labeling. Carbohydrate microarray studies were performed to compare the carbohydrate selectivity of the mannose-recognizing lectin Concanavalin A (ConA) before and after conjugation to fluorescent silica nanoparticles (ConA-fNP). These studies revealed surprisingly low emission intensities upon staining with ConA-fNP compared to those with biotin-ConA/Cy3-streptavidin staining. A series of photophysical and biophysical characterizations of the fNP and ConA-fNP conjugates were performed to probe the low sensitivity from fNP in the microarray assays. Up to 1200 fluorescein (FL) and 80 tetramethylrhodamine (TR) dye molecules were incorporated into 46 nm diameter fNP, yielding emissive brightness values 400 and 35 times larger than the individual dye molecules, respectively. ConA lectin conjugated to carboxylic acid surface-modified nanoparticles covers 15-30% of the fNP surface. The CD spectra and mannose substrate selectivity of ConA conjugated to the fNP differed slightly compared to that of soluble ConA. Although, the high emissive brightness of fNP enhances detection sensitivity for samples with low analyte densities, large fNP diameters limit fNP recruitment and binding to samples with high analyte densities. The high analyte density and nearly two-dimensional target format of carbohydrate microarrays make probe size a critical parameter. In this application, fNP labels afford minimal sensitivity advantage compared to direct dye labeling.

Improving structure-based function prediction using molecular dynamics

The number of molecules with solved three-dimensional structure but unknown function is increasing rapidly. Particularly problematic are novel folds with little detectable similarity to molecules of known function. Experimental assays can determine the functions of such molecules, but are time-consuming and expensive. Computational approaches can identify potential functional sites; however, these approaches generally rely on single static structures and do not use information about dynamics. In fact, structural dynamics can enhance function prediction: we coupled molecular dynamics simulations with structure-based function prediction algorithms that identify Ca(2+) binding sites. When applied to 11 challenging proteins, both methods showed substantial improvement in performance, revealing 22 more sites in one case and 12 more in the other, with a modest increase in apparent false positives. Thus, we show that treating molecules as dynamic entities improves the performance of structure-based function prediction methods.

On the structure of the proton-binding site in the F(o) rotor of chloroplast ATP synthases

The recently reported crystal structures of the membrane-embedded proton-dependent c-ring rotors of a cyanobacterial F(1)F(o) ATP synthase and a chloroplast F(1)F(o) ATP synthase have provided new insights into the mechanism of this essential enzyme. While the overall features of these c-rings are similar, a discrepancy in the structure and hydrogen-bonding interaction network of the H(+) sites suggests two distinct binding modes, potentially reflecting a mechanistic differentiation. Importantly, the conformation of the key glutamate side chain to which the proton binds is also altered. To investigate the nature of these differences, we use molecular dynamics simulations of both c-rings embedded in a phospholipid membrane. We observe that the structure of the c(15) ring from Spirulina platensis is unequivocally stable within the simulation time. By contrast, the proposed structure of the H(+) site in the chloroplast c(14) ring changes rapidly and consistently into that reported for the c(15) ring, indicating that the latter represents a common binding mode. To assess this hypothesis, we have remodeled the c(14) ring by molecular replacement using the published structure factors. The resulting structure provides clear evidence in support of a common binding site conformation and is also considerably improved statistically. These findings, taken together with a sequence analysis of c-subunits in the ATP synthase family, indicate that the so-called proton-locked conformation observed in the c(15) ring may be a common characteristic not only of light-driven systems such as chloroplasts and cyanobacteria but also of a selection of other bacterial species.

Large crystal growth by thermal control allows combined X-ray and neutron crystallographic studies to elucidate the protonation states in Aspergillus flavus urate oxidase

Urate oxidase (Uox) catalyses the oxidation of urate to allantoin and is used to reduce toxic urate accumulation during chemotherapy. X-ray structures of Uox with various inhibitors have been determined and yet the detailed catalytic mechanism remains unclear. Neutron crystallography can provide complementary information to that from X-ray studies and allows direct determination of the protonation states of the active-site residues and substrate analogues, provided that large, well-ordered deuterated crystals can be grown. Here, we describe a method and apparatus used to grow large crystals of Uox (Aspergillus flavus) with its substrate analogues 8-azaxanthine and 9-methyl urate, and with the natural substrate urate, in the presence and absence of cyanide. High-resolution X-ray (1.05-1.20 A) and neutron diffraction data (1.9-2.5 A) have been collected for the Uox complexes at the European Synchrotron Radiation Facility and the Institut Laue-Langevin, respectively. In addition, room temperature X-ray data were also collected in preparation for joint X-ray and neutron refinement. Preliminary results indicate no major structural differences between crystals grown in H(2)O and D(2)O even though the crystallization process is affected. Moreover, initial nuclear scattering density maps reveal the proton positions clearly, eventually providing important information towards unravelling the mechanism of catalysis.

Involvement of water in carbohydrate-protein binding: concanavalin A revisited

Ordered water molecules bound to protein surfaces, or in protein-ligand interfaces, are frequently observed by crystallography. The investigation of the impact of such conserved water molecules on protein stability and ligand affinity requires detailed structural, dynamic, and thermodynamic analyses. Several crystal structures of the legume lectin concanavalin A (Con A) bound to closely related carbohydrate ligands show the presence of a conserved water molecule that mediates ligand binding. Experimental thermodynamic and theoretical studies have examined the role of this conserved water in the complexation of Con A with a synthetic analog of the natural trisaccharide, in which a hydroxyethyl side chain replaces the hydroxyl group at the C-2 position in the central mannosyl residue. Molecular modeling earlier indicated (Clarke, C.; Woods, R. J.; Glushka, J.; Cooper, A.; Nutley, M. A.; Boons, G.-J. J. Am. Chem. Soc. 2001, 123, 12238-12247) that the hydroxyl group in this synthetic side chain could occupy a position equivalent to that of the conserved water, and thus might displace it. An interpretation of the experimental thermodynamic data, which was consistent with the displacement of the conserved water, was also presented. The current work reports the crystal structure of Con A with this synthetic ligand and shows that even though the position and interactions of the conserved water are distorted, this key water is not displaced by the hydroxyethyl moiety. This new structural data provides a firm basis for molecular dynamics simulations and thermodynamic integration calculations whose results indicate that differences in van der Waals contacts (insertion energy), rather than electrostatic interactions (charging energy) are fundamentally responsible for the lower affinity of the synthetic ligand. When combined with the new crystallographic data, this study provides a straightforward interpretation for the lower affinity of the synthetic analog; specifically, that it arises primarily from weaker interactions with the protein via the positionally perturbed conserved water. This interpretation is fully consistent with the experimental observations that the free energy of binding is enthalpy driven, that there is both less enthalpic gain and less entropic penalty for binding the synthetic ligand, relative to the natural trisaccharide, and that the entropic component does not arise from releasing an ordered water molecule from the protein surface to the bulk solvent.

Syntheses, X-ray structures, solid state high-field electron paramagnetic resonance, and density-functional theory investigations on chloro and aqua Mn(II) mononuclear complexes with amino-pyridine pentadentate ligands

The two pentadentate amino-pyridine ligands L5(2) and L5(3) (L5(2) and L5(3) stand for the N-methyl-N,N',N'-tris(2-pyridylmethyl)ethane-1,2-diamine and the N-methyl-N,N',N'-tris(2-pyridylmethyl)propane-1,3-diamine, respectively) were used to synthesize four mononuclear Mn(II) complexes, namely [(L5(2))MnCl](PF6) (1(PF6)), [(L5(3))MnCl](PF6) (2(PF6)), [(L5(2))Mn(OH2)](BPh4)2 (3(BPh4)2), and [(L5(3))Mn(OH2)](BPh4)2 (4(BPh4)2). The X-ray diffraction studies revealed different configurations for the ligand L5(n) (n = 2, 3) depending on the sixth exogenous ligand and/or the counterion. Solid state high-field electron paramagnetic resonance spectra were recorded on complexes 1-4 as on previously described mononuclear Mn(II) systems with tetra- or hexadentate amino-pyridine ligands. Positive and negative axial zero-field splitting (ZFS) parameters D were determined whose absolute values ranged from 0.090 to 0.180 cm(-1). Density-functional theory calculations were performed unraveling that, in contrast with chloro systems, the spin-spin and spin-orbit coupling contributions to the D-parameter are comparable for mixed N,O-coordination sphere complexes.

The catalytic mechanism of an aspartic proteinase explored with neutron and X-ray diffraction

Hydrogen atoms play key roles in enzyme mechanism, but as this study shows, even high-quality X-ray data to a resolution of 1 A cannot directly visualize them. Neutron diffraction, however, can locate deuterium atoms even at resolutions around 2 A. Both neutron and X-ray diffraction data have been used to investigate the transition state of the aspartic proteinase endothiapepsin. The different techniques reveal a different part of the story, revealing the clearest picture yet of the catalytic mechanism by which the enzyme operates. Room temperature neutron and X-ray diffraction data were used in a newly developed joint refinement software package to visualize deuterium atoms within the active site of the enzyme when a gem-diol transition state analogue inhibitor is bound at the active site. These data were also used to estimate their individual occupancy, while analysis of the differences between the bond lengths of the catalytic aspartates was performed using atomic resolution X-ray data. The two methods are in agreement on the protonation state of the active site with a transition state analogue inhibitor bound confirming the catalytic mechanism at which the enzyme operates.

Structure of a lectin from Canavalia gladiata seeds: new structural insights for old molecules

BACKGROUND

Lectins are mainly described as simple carbohydrate-binding proteins. Previous studies have tried to identify other binding sites, which possible recognize plant hormones, secondary metabolites, and isolated amino acid residues. We report the crystal structure of a lectin isolated from Canavalia gladiata seeds (CGL), describing a new binding pocket, which may be related to pathogen resistance activity in ConA-like lectins; a site where a non-protein amino-acid, alpha-aminobutyric acid (Abu), is bound.

RESULTS

The overall structure of native CGL and complexed with alpha-methyl-mannoside and Abu have been refined at 2.3 A and 2.31 A resolution, respectively. Analysis of the electron density maps of the CGL structure shows clearly the presence of Abu, which was confirmed by mass spectrometry.

CONCLUSION

The presence of Abu in a plant lectin structure strongly indicates the ability of lectins on carrying secondary metabolites. Comparison of the amino acids composing the site with other legume lectins revealed that this site is conserved, providing an evidence of the biological relevance of this site. This new action of lectins strengthens their role in defense mechanisms in plants.

Comparative analysis of protein structure alignments

Background

Several methods are currently available for the comparison of protein structures. These methods have been analysed regarding the performance in the identification of structurally/evolutionary related proteins, but so far there has been less focus on the objective comparison between the alignments produced by different methods.

Results

We analysed and compared the structural alignments obtained by different methods using three sets of pairs of structurally related proteins. The first set corresponds to 355 pairs of remote homologous proteins according to the SCOP database (ASTRAL40 set). The second set was derived from the SISYPHUS database and includes 69 protein pairs (SISY set). The third set consists of 40 pairs that are challenging to align (RIPC set). The alignment of pairs of this set requires indels of considerable number and size and some of the proteins are related by circular permutations, show extensive conformational variability or include repetitions. Two standard methods (CE and DALI) were applied to align the proteins in the ASTRAL40 set. The extent of structural similarity identified by both methods is highly correlated and the alignments from the two methods agree on average in more than half of the aligned positions. CE, DALI, as well as four additional methods (FATCAT, MATRAS, C_α-match and SHEBA) were then compared using the SISY and RIPC sets. The accuracy of the alignments was assessed by comparison to reference alignments. The alignments generated by the different methods on average match more than half of the reference alignments in the SISY set. The alignments obtained in the more challenging RIPC set tend to differ considerably and match reference alignments less successfully than the SISY set alignments.

Conclusion

The alignments produced by different methods tend to agree to a considerable extent, but the agreement is lower for the more challenging pairs. The results for the comparison to reference alignments are encouraging, but also indicate that there is still room for improvement.

Manganese binding to the 23 kDa extrinsic protein of Photosystem II

The recombinant form of the extrinsic 23 kDa protein (psbP) of Photosystem II (PSII) was studied with respect to its capability to bind Mn. The stoichiometry was determined to be one manganese bound per protein. A very high binding constant, K(A)=10(-17) M(-1), was determined by dialysis of the Mn containing protein against increasing EDTA concentration. High Field EPR spectroscopy was used to distinguish between specific symmetrically ligated Mn(II) from those non-specifically Mn(II) attached to the protein surface. Upon Mn binding PsbP exhibited fluorescence emission with maxima at 415 and 435 nm when tryptophan residues were excited. The yield of this blue fluorescence was variable from sample to sample. It was likely that different conformational states of the protein were responsible for this variability. The importance of Mn binding to PsbP in the context of photoactivation of PSII is discussed.