New methods for sedimentation and diffusion analysis of macromolecular structure

Methods are presented to acquire data from analytical ultracentrifugation experiments by computer using the absorption optical scanning system of the Beckman Model-E ultracentrifuge. A computer program was written which analyzes sedimentation velocity experiments by the van Holde - Weischet method and by the second moment method. The van Holde - Weischet method allows a high resolution analysis of sedimentation velocity data by eliminating the effects of diffusion on the shape of the moving boundary to provide sedimentation coefficients for a heterogeneous composition of a sample. The second moment method obtains the sedimentation coefficient by calculating the second moment point, by which the sedimentation coefficient is defined. Since it is impractical to manually analyze sedimentation velocity data by this method, these computer programs make an important analysis method available to the researcher. Using this computer program, it is now possible to analyze data to a higher resolution and accuracy than manual analysis of stripchart recordings would permit. Moreover, the time required for the analysis is greatly reduced. Data from sedimentation equilibrium experiments are analyzed by x² minimization. Further, a program was written for the acquisition of data to measure diffusion coefficients from quasi elastic light scattering experiments with a Langley Ford correlator. The analysis of autocorrelation spectra from light scattering experiments is performed by the Levenberg - Marquardt method, which allows fitting of data to nonlinear models. The model used allows the analysis of multicomponent systems by fitting to a sum of exponentials and a baseline. Traditional analysis of autocorrelation data by hand was limited to least squares fitting of the data to a linear model of one component without an optimized baseline, often an unrealistic approximation of the system. Analysis of autocorrelation data by nonlinear curve fitting increases both the accuracy and amount of data that can be analyzed. The development of the PPOL-1 208-n series of plasmids and of the miniplasmid pMX is described. These plasmids were designed to allow studies of in vitro transcription and chromatin structure after reconstitution with histones. The plasmids themselves were analyzed by sedimentation and diffusion studies using the computer programs. Sedimentation data is presented which suggests a new method for rapid estimation of S₀ (the sedimentation coefficient at zero concentration) for molecules which show a concentration dependency of the sedimentation coefficient. This is accomplished by linearly extrapolating van Holde Weischet distributions to zero concentration. Manual analysis of sedimentation velocity experiments to determine nonideality contributions required several experiments, computer analysis can provide this information in a single experiment due to the increased resolution of the method. Diffusion data for this plasmid DNA is used to demonstrate the feasibility of the multicomponent analysis presented here. Also, sedimentation measurements were carried out on reconstituted chromatin and on the effects of ethidium bromide on reconstituted chromatin. The programs were used to demonstrate significant changes in chromatin structure upon ethidium bromide binding. These changes involved the reduction of S of reconstituted plasmids upon addition of ethidium bromide as well as a reduction of heterogeneity of the sample. The data indicates the possibility of a forced exchange of nucleosomes between plasmids, as well as conformational changes in the chromatin structure

Structure and Activation Mechanism of the Drosophila Initiator Caspase Dronc

Activation of an initiator caspase is essential to the execution of apoptosis. The molecular mechanisms by which initiator caspases are activated remain poorly understood. Here we demonstrate that the autocatalytic cleavage of Dronc, an important initiator caspase in Drosophila, results in a drastic enhancement of its catalytic activity in vitro. The autocleaved Dronc forms a homodimer, whereas the uncleaved Dronc zymogen exists exclusively as a monomer. Thus the autocatalytic cleavage in Dronc induces its stable dimerization, which presumably allows the two adjacent monomers to mutually stabilize their active sites, leading to activation. Crystal structure of a prodomain-deleted Dronc zymogen, determined at 2.5 Å resolution, reveals an unproductive conformation at the active site, which is consistent with the observation that the zymogen remains catalytically inactive. This study revealed insights into mechanism of Dronc activation, and in conjunction with other observations, suggests diverse mechanisms for the activation of initiator caspases

Ultrascan solution modeler: integrated hydrodynamic parameter and small angle scattering computation and fitting tools

This is a preprint of a paper in the proceedings of the XSEDE12 conference, held July 16-19, 2012 in Chicago, IL. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.UltraScan Solution Modeler (US-SOMO) processes atomic and lower-resolution bead model representations of biological and other macromolecules to compute various hydrodynamic parameters, such as the sedimentation and diffusion coefficients, relaxation times and intrinsic viscosity, and small angle scattering curves, that contribute to our understanding of molecular structure in solution. Knowledge of biological macromolecules' structure aids researchers in understanding their function as a path to disease prevention and therapeutics for conditions such as cancer, thrombosis, Alzheimer's disease and others. US-SOMO provides a convergence of experimental, computational, and modeling techniques, in which detailed molecular structure and properties are determined from data obtained in a range of experimental techniques that, by themselves, give incomplete information. Our goal in this work is to develop the infrastructure and user interfaces that will enable a wide range of scientists to carry out complicated experimental data analysis techniques on XSEDE. Our user community predominantly consists of biophysics and structural biology researchers. A recent search on PubMed reports 9,205 papers in the decade referencing the techniques we support. We believe our software will provide these researchers a convenient and unique framework to refine structures, thus advancing their research. The computed hydrodynamic parameters and scattering curves are screened against experimental data, effectively pruning potential structures into equivalence classes. Experimental methods may include analytical ultracentrifugation, dynamic light scattering, small angle X-ray and neutron scattering, NMR, fluorescence spectroscopy, and others. One source of macromolecular models is X-ray crystallography. However, the conformation in solution may not match that observed in the crystal form. Using computational techniques, an initial fixed model can be expanded into a search space utilizing high temperature molecular dynamic approaches or stochastic methods such as Brownian dynamics. The number of structures produced can vary greatly, ranging from hundreds to tens of thousands or more. This introduces a number of cyberinfrastructure challenges. Computing hydrodynamic parameters and small angle scattering curves can be computationally intensive for each structure, and therefore cluster compute resources are essential for timely results. Input and output data sizes can vary greatly from less than 1 MB to 2 GB or more. Although the parallelization is trivial, along with data size variability there is a large range of compute sizes, ranging from one to potentially thousands of cores with compute time of minutes to hours. In addition to the distributed computing infrastructure challenges, an important concern was how to allow a user to conveniently submit, monitor and retrieve results from within the C++/Qt GUI application while maintaining a method for authentication, approval and registered publication usage throttling. Middleware supporting these design goals has been integrated into the application with assistance from the Open Gateway Computing Environments (OGCE) collaboration team. The approach was tested on various XSEDE clusters and local compute resources. This paper reviews current US-SOMO functionality and implementation with a focus on the newly deployed cluster integration.This work was supported by NIH grant K25GM090154 to EB, NSF grant OCI-1032742 to MP, NSF grant TG-MCB070040N to BD, and NIH grant RR-022200 to B

Science Gateway Operational Sustainability: Adopting a Platform-as-a Service Approach

The authors discuss their position on operational sustainability for web-based science gateways

Two-dimensional grid optimization for sedimentation velocity analysis in the analytical ultracentrifuge

Accepted author manuscriptSedimentation velocity experiments performed in the analytical ultracentrifuge are modeled using finite-element solutions of the Lamm equation. During modeling, three fundamental parameters are optimized: the sedimentation coefficients, the diffusion coefficients, and the partial concentrations of all solutes present in a mixture. A general modeling approach consists of fitting the partial concentrations of solutes defined in a two-dimensional grid of sedimentation and diffusion coefficient combinations that cover the range of possible solutes for a given mixture. An increasing number of grid points increase the resolution of the model produced by the subsequent analysis, with denser grids giving rise to a very large system of equations. Here, we evaluate the efficiency and resolution of several regular grids and show that traditionally defined grids tend to provide inadequate coverage in one region of the grid, while at the same time being computationally wasteful in other sections of the grid. We describe a rapid and systematic approach for generating efficient two-dimensional analysis grids that balance optimal information content and model resolution for a given signal-to-noise ratio with improved calculation efficiency. These findings are general and apply to one- and two-dimensional grids, although they no longer represent regular grids. We provide a recipe for an improved grid-point spacing in both directions which eliminates unnecessary points, while at the same time providing a more uniform resolution that can be scaled based on the stochastic noise in the experimental data.Ye

Structural basis for L27 domain‐mediated assembly of signaling and cell polarity complexes

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/102252/1/emboj7600294.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/102252/2/emboj7600294-sup-0001.pd

Nanoscale structure determination of Murray Valley encephalitis and Powassan virus non-coding RNAs

Open access article. Creative Commons Attribution 4.0 International License (CC BY 4.0) appliesViral infections are responsible for numerous deaths worldwide. Flaviviruses, which contain RNA as their genetic material, are one of the most pathogenic families of viruses. There is an increasing amount of evidence suggesting that their 5’ and 3’ non-coding terminal regions are critical for their survival. Information on their structural features is essential to gain detailed insights into their functions and interactions with host proteins. In this study, the 5’ and 3’ terminal regions of Murray Valley encephalitis virus and Powassan virus were examined using biophysical and computational modeling methods. First, we used size exclusion chromatography and analytical ultracentrifuge methods to investigate the purity of in-vitro transcribed RNAs. Next, we employed small-angle X-ray scattering techniques to study solution conformation and low-resolution structures of these RNAs,which suggest that the 3’ terminal regions are highly extended as compared to the 5’ terminal regions for both viruses. Using computational modeling tools, we reconstructed 3-dimensional structures of each RNA fragment and compared them with derived small-angle X-ray scattering low-resolution structures. This approach allowed us to reinforce that the 5’ terminal regions adopt more dynamic structures compared to the mainly double-stranded structures of the 3’ terminal regions.Ye

Structural studies of cerebral cavernous malformations 2 (CCM2) reveal a folded helical domain at its C-terminus

AbstractCerebral cavernous malformations (CCM) are neurovascular dysplasias affecting up to 0.5% of the population. Mutations in the CCM2 gene are associated with acquisition of CCM. We identify a previously uncharacterized domain at the C-terminus of CCM2 and determine its 1.9Å resolution crystal structure. Because this domain is structurally homologous to the N-terminal domain of harmonin, we name it the CCM2 harmonin-homology domain or HHD. CCM2 HHD is observed in two conformations, and we employ analytical ultracentrifugation to test its oligomerization. Additionally, CCM2 HHD contains an unusually long 13-residue 310 helix. This study provides the first structural characterization of CCM2.Structured summary of protein interactionsCCM2 binds to CCM3 by pull down (View interaction)CCM2 and CCM2 bind by X-ray crystallography (View interaction)CCM2 and CCM2 bind by molecular sieving (View interaction

Novel combinations of experimental and computational analysis tested on the binding of metalloprotoporphyrins to albumin

Accepted author manuscriptThe evidence that Human Serum Albumin (HSA) binds metal ions and organometallic compounds has generated interest in its physiological role as a metalloprotein and as a vehicle for synthetic biology applications (e.g., synthetic blood and solar energy conversion). HSA has been shown to bind metallo-porphyrins, however, the structural details of such interactions are available only for the HSA:heme complex. A typical challenge for studying the interaction of proteins with metalloporphyrins is the poor solubility of the ligands that affect the characterization the complexes. The manuscript shows that a combination of dialysis and centrifugation yields aqueous solutions that contain >90% HSA:porphyrin complexes and virtually eliminate aggregated ligands. The removal of aggregates increases the quality of the optical spectroscopy data which, in turn, yield more accurate binding constants (~0.1 and 2.1 × 106 M−1) and reveal FRET between Trp214 and the porphyrins. The Trp-porphyrin distance was estimated to be within the 28–34 Å range and was used to guide the search of binding sites through a novel feedback approach with docking simulations. Results suggest while some protoporphyrins (metal-free, Fe(III)PPIX and Mg(II)PPIX) bind HSA at the heme site, others (Zn(II)PPIX, Mn(III)PPIX and Sn(IV)PPIX) are more likely to bind the Cys34.Ye

Nanometer To Millimeter Scale Peptide-porphyrin Materials

AQ-Pal14 is a 30-residue polypeptide that was designed to form an alpha-helical coiled coil that contains a metal-binding 4-pyridylalanine residue on its solvent-exposed surface. However, characterization of this peptide shows that it exists as a three-stranded coiled coil, not a two-stranded one as predicted from its design. Reaction with cobalt(III) protoporphyrin IX (Co-PPIX) produces a six-coordinate Co-PPIX(AQ-Pal 14)(2) species that creates two coiled-coil oligomerization domains Coordinated to opposite laces of the porphyrin ring. It is found that this species undergoes a buffer-dependent Self-assembly process: nanometer-scale globular materials were formed when these components were reacted in unbuffered H(2)O, while millimeter-scale, rod-like materials were prepared when the reaction was performed in phosphate buffer (20 mM, pH 7). It is suggested that assembly of the globular material is dictated by the conformational properties of the coiled-coil forming AQ-Pal14 peptide, whereas that a the rod-like material involves interactions between Co-PPIX and phosphate ion