Protein structure prediction servers at University College London

A number of state-of-the-art protein structure prediction servers have been developed by researchers working in the Bioinformatics Unit at University College London. The popular PSIPRED server allows users to perform secondary structure prediction, transmembrane topology prediction and protein fold recognition. More recent servers include DISOPRED for the prediction of protein dynamic disorder and DomPred for domain boundary prediction.

A combined BIE-FE method for the Stokes equations

A numerical algorithm for the biharmonic equation in domains with piecewise smooth boundaries is presented. It is intended for problems describing the Stokes flow in the situations where one has corners or cusps formed by parts of the domain boundary and, due to the nature of the boundary conditions on these parts of the boundary, these regions have a global effect on the shape of the whole domain and hence have to be resolved with sufficient accuracy. The algorithm combines the boundary integral equation method for the main part of the flow domain and the finite-element method which is used to resolve the corner/cusp regions. Two parts of the solution are matched along a numerical ‘internal interface’ or, as a variant, two interfaces, and they are determined simultaneously by inverting a combined matrix in the course of iterations. The algorithm is illustrated by considering the flow configuration of ‘curtain coating’, a flow where a sheet of liquid impinges onto a moving solid substrate, which is particularly sensitive to what happens in the corner region formed, physically, by the free surface and the solid boundary. The ‘moving contact line problem’ is addressed in the framework of an earlier developed interface formation model which treats the dynamic contact angle as part of the solution, as opposed to it being a prescribed function of the contact line speed, as in the so-called ‘slip models’. Keywords: Dynamic contact angle; finite elements; free surface flows; hybrid numerical technique; Stokes equations.

Boundary layer structure and decoupling from synoptic scale flow during NAMBLEX

This paper presents an overview of the meteorology and planetary boundary layer structure observed during the NAMBLEX field campaign to aid interpretation of the chemical and aerosol measurements. The campaign has been separated into five periods corresponding to the prevailing synoptic condition. Comparisons between meteorological measurements ( UHF wind profiler, Doppler sodar, sonic aneometers mounted on a tower at varying heights and a standard anemometer) and the ECMWF analysis at 10 m and 1100 m identified days when the internal boundary layer was decoupled from the synoptic flow aloft. Generally the agreement was remarkably good apart from during period one and on a few days during period four when the diurnal swing in wind direction implies a sea/land breeze circulation near the surface. During these periods the origin of air sampled at Mace Head would not be accurately represented by back trajectories following the winds resolved in ECMWF analyses. The wind profiler observations give a detailed record of boundary layer structure including an indication of its depth, average wind speed and direction. Turbulence statistics have been used to assess the height to which the developing internal boundary layer, caused by the increased surface drag at the coast, reaches the sampling location under a wide range of marine conditions. Sampling conducted below 10 m will be impacted by emission sources at the shoreline in all wind directions and tidal conditions, whereas sampling above 15 m is unlikely to be affected in any of the wind directions and tidal heights sampled during the experiment.

The Klein-Gordon equation in a domain with time-dependent boundary

We solve a Dirichlet boundary value problem for the Klein–Gordon equation posed in a time-dependent domain. Our approach is based on a general transform method for solving boundary value problems for linear and integrable nonlinear PDE in two variables. Our results consist of the inversion formula for a generalized Fourier transform, and of the application of this generalized transform to the solution of the boundary value problem.

Nuclear magnetic resonance structure shows that the severe acute respiratory syndrome coronavirus-unique domain contains a macrodomain fold

The nuclear magnetic resonance (NMR) structure of a central segment of the previously annotated severe acute respiratory syndrome (SARS)-unique domain (SUD-M, for "middle of the SARS-unique domain") in SARS coronavirus (SARS-CoV) nonstructural protein 3 (nsp3) has been determined. SUD-M(513-651) exhibits a macrodomain fold containing the nsp3 residues 528 to 648, and there is a flexibly extended N-terminal tail with the residues 513 to 527 and a C-terminal flexible tail of residues 649 to 651. As a follow-up to this initial result, we also solved the structure of a construct representing only the globular domain of residues 527 to 651 [SUD-M(527-651)]. NMR chemical shift perturbation experiments showed that SUD-M(527-651) binds single-stranded poly(A) and identified the contact area with this RNA on the protein surface, and electrophoretic mobility shift assays then confirmed that SUD-M has higher affinity for purine bases than for pyrimidine bases. In a further search for clues to the function, we found that SUD-M(527-651) has the closest three-dimensional structure homology with another domain of nsp3, the ADP-ribose-1 ''-phosphatase nsp3b, although the two proteins share only 5% sequence identity in the homologous sequence regions. SUD-M(527-651) also shows three-dimensional structure homology with several helicases and nucleoside triphosphate-binding proteins, but it does not contain the motifs of catalytic residues found in these structural homologues. The combined results from NMR screening of potential substrates and the structure-based homology studies now form a basis for more focused investigations on the role of the SARS-unique domain in viral infection.

Nuclear magnetic resonance structure of the nucleic acid-binding domain of severe acute respiratory syndrome coronavirus nonstructural protein 3

The nuclear magnetic resonance (NMR) structure of a globular domain of residues 1071 to 1178 within the previously annotated nucleic acid-binding region (NAB) of severe acute respiratory syndrome coronavirus nonstructural protein 3 (nsp3) has been determined, and N- and C-terminally adjoining polypeptide segments of 37 and 25 residues, respectively, have been shown to form flexibly extended linkers to the preceding globular domain and to the following, as yet uncharacterized domain. This extension of the structural coverage of nsp3 was obtained from NMR studies with an nsp3 construct comprising residues 1066 to 1181 [ nsp3(1066-1181)] and the constructs nsp3(1066-1203) and nsp3(1035-1181). A search of the protein structure database indicates that the globular domain of the NAB represents a new fold, with a parallel four-strand beta-sheet holding two alpha-helices of three and four turns that are oriented antiparallel to the beta-strands. Two antiparallel two-strand beta-sheets and two 3(10)-helices are anchored against the surface of this barrel-like molecular core. Chemical shift changes upon the addition of single-stranded RNAs (ssRNAs) identified a group of residues that form a positively charged patch on the protein surface as the binding site responsible for the previously reported affinity for nucleic acids. This binding site is similar to the ssRNA-binding site of the sterile alpha motif domain of the Saccharomyces cerevisiae Vts1p protein, although the two proteins do not share a common globular fold.

NMR structure shows that the SARS-unique domain contains a macrodomain fold

The NMR structure of a central segment of the previously annotated "SARS-unique domain" (SUD-M; "middle of the SARS-unique domain") in the SARS coronavirus (SARS-CoV) non-structural protein 3 (nsp3) has been determined. SUD-M(513-651) exhibits a macrodomain fold containing the nsp3-residues 528-648, and there is a flexibly extended N-terminal tail with the residues 513-527 and a C-terminal flexible tail of residues 649-651. As a follow-up to this initial result, we also solved the structure of a construct representing only the globular domain of residues 527-651 [SUD-M(527-651)]. NMR chemical shift perturbation experiments showed that SUD-M(527-651) binds single-stranded poly-A and identified the contact area with this RNA on the protein surface, and electrophoretic mobility shift assays then confirmed that SUD-M has higher affinity for purine bases than for pyrimidine bases. In further search for clues to the function, we found that SUD-M(527-651) has the closest three-dimensional structure homology with another domain of nsp3, the ADP-ribose-1''-phosphatase nsp3b, although the two proteins share only 5% sequence identity in the homologous sequence regions. SUD-M(527-651) also shows 3D structure homology with several helicases and NTP-binding proteins, but it does not contain the motifs of catalytic residues found in these structural homologues. The combined results from NMR screening of potential substrates and the structure-based homology studies now form a basis for more focused investigations on the role of the SARS-unique domain in viral infection.

Nuclear magnetic resonance structure of the N-terminal domain of nonstructural protein 3 from the severe acute respiratory syndrome coronavirus

This paper describes the structure determination of nsp3a, the N-terminal domain of the severe acute respiratory syndrome coronavirus (SARS-CoV) nonstructural protein 3. nsp3a exhibits a ubiquitin-like globular fold of residues 1 to 112 and a flexibly extended glutamic acid-rich domain of residues 113 to 183. In addition to the four beta-strands and two alpha-helices that are common to ubiquitin-like folds, the globular domain of nsp3a contains two short helices representing a feature that has not previously been observed in these proteins. Nuclear magnetic resonance chemical shift perturbations showed that these unique structural elements are involved in interactions with single-stranded RNA. Structural similarities with proteins involved in various cell-signaling pathways indicate possible roles of nsp3a in viral infection and persistence.

The structure of echovirus type 12 bound to a two-domain fragment of its cellular attachment protein decay-accelerating factor (CD 55)

Echovirus type 12 (EV12), an enterovirus of the Picornaviridae family, uses the complement regulator, decay-accelerating factor (DAF, CD55) as a cellular receptor. We have calculated a three-dimensional reconstruction of EV12 bound to a fragment of DAF, consisting of short consensus repeat domains 3 and 4, from cryo-negative stain electron microscopy data (EMD #1057). This shows that, as for an earlier reconstruction of the related echovirus type 7 bound to DAF, attachment is not within the viral canyon but occurs close to the two-fold symmetry axes. Despite this general similarity, our reconstruction reveals a receptor interaction that is quite different from that observed for EV7. Fitting of the crystallographic co-ordinates for DAF34 and EV11 into the reconstruction shows a close agreement between the crystal structure of the receptor fragment and the density for the virus-bound receptor, allowing unambiguous positioning of the receptor with respect to the virion (PDB #1UPN). Our finding that the mode of virus-receptor interaction in EV12 is distinct from that seen for EV7 raises interesting questions regarding the evolution and biological significance of the DAF-binding phenotype in these viruses.

Rapid protein domain assignment from amino acid sequence using predicted secondary structure

The elucidation of the domain content of a given protein sequence in the absence of determined structure or significant sequence homology to known domains is an important problem in structural biology. Here we address how successfully the delineation of continuous domains can be accomplished in the absence of sequence homology using simple baseline methods, an existing prediction algorithm (Domain Guess by Size), and a newly developed method (DomSSEA). The study was undertaken with a view to measuring the usefulness of these prediction methods in terms of their application to fully automatic domain assignment. Thus, the sensitivity of each domain assignment method was measured by calculating the number of correctly assigned top scoring predictions. We have implemented a new continuous domain identification method using the alignment of predicted secondary structures of target sequences against observed secondary structures of chains with known domain boundaries as assigned by Class Architecture Topology Homology (CATH). Taking top predictions only, the success rate of the method in correctly assigning domain number to the representative chain set is 73.3%. The top prediction for domain number and location of domain boundaries was correct for 24% of the multidomain set (±20 residues). These results have been put into context in relation to the results obtained from the other prediction methods assessed

Structure of the ROC domain from the Parkinson's disease-associated leucine-rich repeat kinase 2 reveals a dimeric GTPase

Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common cause of Parkinson's disease (PD). LRRK2 contains a Ras of complex proteins (ROC) domain that may act as a GTPase to regulate its protein kinase activity. The structure of ROC and the mechanism(s) by which it regulates kinase activity are not known. Here, we report the crystal structure of the LRRK2 ROC domain in complex with GDP-Mg2+ at 2.0-Å resolution. The structure displays a dimeric fold generated by extensive domain-swapping, resulting in a pair of active sites constructed with essential functional groups contributed from both monomers. Two PD-associated pathogenic residues, R1441 and I1371, are located at the interface of two monomers and provide exquisite interactions to stabilize the ROC dimer. The structure demonstrates that loss of stabilizing forces in the ROC dimer is likely related to decreased GTPase activity resulting from mutations at these sites. Our data suggest that the ROC domain may regulate LRRK2 kinase activity as a dimer, possibly via the C-terminal of ROC (COR) domain as a molecular hinge. The structure of the LRRK2 ROC domain also represents a signature from a previously undescribed class of GTPases from complex proteins and results may provide a unique molecular target for therapeutics in PD.

Evaluation of a boundary integral representation for the conformal mapping of the unit disk onto a simply-connected domain

A representation of the conformal mapping g of the interior or exterior of the unit circle onto a simply-connected domain Ω as a boundary integral in terms ofƒ|∂Ω is obtained, whereƒ :=g -l. A product integration scheme for the approximation of the boundary integral is described and analysed. An ill-conditioning problem related to the domain geometry is discussed. Numerical examples confirm the conclusions of this discussion and support the analysis of the quadrature scheme.

Structure of the planetary boundary layer over southeast England: modeling and measurements

The Weather Research and Forecasting model was applied to analyze variations in the planetary boundary layer (PBL) structure over Southeast England including central and suburban London. The parameterizations and predictive skills of two nonlocal mixing PBL schemes, YSU and ACM2, and two local mixing PBL schemes, MYJ and MYNN2, were evaluated over a variety of stability conditions, with model predictions at a 3 km grid spacing. The PBL height predictions, which are critical for scaling turbulence and diffusion in meteorological and air quality models, show significant intra-scheme variance (> 20%), and the reasons are presented. ACM2 diagnoses the PBL height thermodynamically using the bulk Richardson number method, which leads to a good agreement with the lidar data for both unstable and stable conditions. The modeled vertical profiles in the PBL, such as wind speed, turbulent kinetic energy (TKE), and heat flux, exhibit large spreads across the PBL schemes. The TKE predicted by MYJ were found to be too small and show much less diurnal variation as compared with observations over London. MYNN2 produces better TKE predictions at low levels than MYJ, but its turbulent length scale increases with height in the upper part of the strongly convective PBL, where it should decrease. The local PBL schemes considerably underestimate the entrainment heat fluxes for convective cases. The nonlocal PBL schemes exhibit stronger mixing in the mean wind fields under convective conditions than the local PBL schemes and agree better with large-eddy simulation (LES) studies.

Observations of urban boundary layer structure during a strong urban heat island event

It has long been known that the urban surface energy balance is different to that of a rural surface, and that heating of the urban surface after sunset gives rise to the Urban Heat Island (UHI). Less well known is how flow and turbulence structure above the urban surface are changed during different phases of the urban boundary layer (UBL). This paper presents new observations above both an urban and rural surface and investigates how much UBL structure deviates from classical behaviour. A 5-day, low wind, cloudless, high pressure period over London, UK, was chosen for analysis, during which there was a strong UHI. Boundary layer evolution for both sites was determined by the diurnal cycle in sensible heat flux, with an extended decay period of approximately 4 h for the convective UBL. This is referred to as the “Urban Convective Island” as the surrounding rural area was already stable at this time. Mixing height magnitude depended on the combination of regional temperature profiles and surface temperature. Given the daytime UHI intensity of 1.5∘C, combined with multiple inversions in the temperature profile, urban and rural mixing heights underwent opposite trends over the period, resulting in a factor of three height difference by the fifth day. Nocturnal jets undergoing inertial oscillations were observed aloft in the urban wind profile as soon as the rural boundary layer became stable: clear jet maxima over the urban surface only emerged once the UBL had become stable. This was due to mixing during the Urban Convective Island reducing shear. Analysis of turbulent moments (variance, skewness and kurtosis) showed “upside-down” boundary layer characteristics on some mornings during initial rapid growth of the convective UBL. During the “Urban Convective Island” phase, turbulence structure still resembled a classical convective boundary layer but with some influence from shear aloft, depending on jet strength. These results demonstrate that appropriate choice of Doppler lidar scan patterns can give detailed profiles of UBL flow. Insights drawn from the observations have implications for accuracy of boundary conditions when simulating urban flow and dispersion, as the UBL is clearly the result of processes driven not only by local surface conditions but also regional atmospheric structure.

Turbulent structure and scaling of the inertial subrange in a stratocumulus-topped boundary layer observed by a Doppler lidar

The turbulent structure of a stratocumulus-topped marine boundary layer over a 2-day period is observed with a Doppler lidar at Mace Head in Ireland. Using profiles of vertical velocity statistics, the bulk of the mixing is identified as cloud driven. This is supported by the pertinent feature of negative vertical velocity skewness in the sub-cloud layer which extends, on occasion, almost to the surface. Both coupled and decoupled turbulence characteristics are observed. The length and timescales related to the cloud-driven mixing are investigated and shown to provide additional information about the structure and the source of the mixing inside the boundary layer. They are also shown to place constraints on the length of the sampling periods used to derive products, such as the turbulent dissipation rate, from lidar measurements. For this, the maximum wavelengths that belong to the inertial subrange are studied through spectral analysis of the vertical velocity. The maximum wavelength of the inertial subrange in the cloud-driven layer scales relatively well with the corresponding layer depth during pronounced decoupled structure identified from the vertical velocity skewness. However, on many occasions, combining the analysis of the inertial subrange and vertical velocity statistics suggests higher decoupling height than expected from the skewness profiles. Our results show that investigation of the length scales related to the inertial subrange significantly complements the analysis of the vertical velocity statistics and enables a more confident interpretation of complex boundary layer structures using measurements from a Doppler lidar.