Borries Demeler

Structure of the Hsp110:Hsc70 Nucleotide Exchange Machine

Hsp70s mediate protein folding, translocation, and macromolecular complex remodeling reactions. Their activities are regulated by proteins that exchange ADP for ATP from the nucleotide-binding domain (NBD) of the Hsp70. These nucleotide exchange factors (NEFs) include the Hsp110s, which are themselves members of the Hsp70 family. We report the structure of an Hsp110:Hsc70 nucleotide exchange complex. The complex is characterized by extensive protein:protein interactions and symmetric bridging interactions between the nucleotides bound in each partner proteins NBD. An electropositive pore allows nucleotides to enter and exit the complex. The role of nucleotides in complex formation and dissociation, and the effects of the protein:protein interactions on nucleotide exchange, can be understood in terms of the coupled effects of the nucleotides and protein:protein interactions on the open-closed isomerization of the NBDs. The symmetrical interactions in the complex may model other Hsp70 family heterodimers in which two Hsp70s reciprocally act as NEFs.

Direct Sedimentation Analysis of Interference Optical Data in Analytical Ultracentrifugation

Sedimentation data acquired with the interference optical scanning system of the Optima XL-I analytical ultracentrifuge can exhibit time-invariant noise components, as well as small radial-invariant baseline offsets, both superimposed onto the radial fringe shift data resulting from the macromolecular solute distribution. A well-established method for the interpretation of such ultracentrifugation data is based on the analysis of time-differences of the measured fringe profiles, such as employed in the g(s*) method. We demonstrate how the technique of separation of linear and nonlinear parameters can be used in the modeling of interference data by unraveling the time-invariant and radial-invariant noise components. This allows the direct application of the recently developed approximate analytical and numerical solutions of the Lamm equation to the analysis of interference optical fringe profiles. The presented method is statistically advantageous since it does not require the differentiation of the data and the model functions. The method is demonstrated on experimental data and compared with the results of a g(s*) analysis. It is also demonstrated that the calculation of time-invariant noise components can be useful in the analysis of absorbance optical data. They can be extracted from data acquired during the approach to equilibrium, and can be used to increase the reliability of the results obtained from a sedimentation equilibrium analysis.

Identification and interpretation of complexity in sedimentation velocity boundaries

Synthetic sedimentation velocity boundaries were generated using finite-element solutions to the original and modified forms of the Lamm equation. Situations modeled included ideal single- and multicomponent samples, concentration-dependent samples, noninteracting multicomponent samples, and reversibly self-associating samples. Synthetic boundaries subsequently were analyzed using the method of van Holde and Weischet, and results were compared against known input parameters. Results indicate that this analytical method provides rigorous diagnostics for virtually every type of sample complexity encountered experimentally. Accordingly, both the power and utility of sedimentation velocity experiments have been significantly expanded.

A two-dimensional spectrum analysis for sedimentation velocity experiments of mixtures with heterogeneity in molecular weight and shape

We report a model-independent analysis approach for fitting sedimentation velocity data which permits simultaneous determination of shape and molecular weight distributions for mono- and polydisperse solutions of macromolecules. Our approach allows for heterogeneity in the frictional domain, providing a more faithful description of the experimental data for cases where frictional ratios are not identical for all components. Because of increased accuracy in the frictional properties of each component, our method also provides more reliable molecular weight distributions in the general case. The method is based on a fine grained two-dimensional grid search over s and f/f0, where the grid is a linear combination of whole boundary models represented by finite element solutions of the Lamm equation with sedimentation and diffusion parameters corresponding to the grid points. A Monte Carlo approach is used to characterize confidence limits for the determined solutes. Computational algorithms addressing the very large memory needs for a fine grained search are discussed. The method is suitable for globally fitting multi-speed experiments, and constraints based on prior knowledge about the experimental system can be imposed. Time- and radially invariant noise can be eliminated. Serial and parallel implementations of the method are presented. We demonstrate with simulated and experimental data of known composition that our method provides superior accuracy and lower variance fits to experimental data compared to other methods in use today, and show that it can be used to identify modes of aggregation and slow polymerization.

Ag44(SR)304−: a silver–thiolate superatom complex

Intensely and broadly absorbing nanoparticles (IBANs) of silver protected by arylthiolates were recently synthesized and showed unique optical properties, yet question of their dispersity and their molecular formulas remained. Here IBANs are identified as a superatom complex with a molecular formula of Ag(44)(SR)(30)(4-) and an electron count of 18. This molecular character is shared by IBANs protected by 4-fluorothiophenol or 2-naphthalenethiol. The molecular formula and purity is determined by mass spectrometry and confirmed by sedimentation velocity-analytical ultracentrifugation. The data also give preliminary indications of a unique structure and environment for Ag(44)(SR)(30)(4-).

Cytotoxic Cell Granule-mediated Apoptosis CHARACTERIZATION OF THE MACROMOLECULAR COMPLEX OF GRANZYME B WITH SERGLYCIN

We have recently shown that the physiological mediator of granule-mediated apoptosis is a macromolecular complex of granzymes and perforin complexed with the chondroitin-sulfate proteoglycan, serglycin (Metkar, S. S., Wang, B., Aguilar-Santelises, M., Raja, S. M., Uhlin-Hansen, L., Podack, E., Trapani, J. A., and Froelich, C. J. (2002)Immunity 16, 417–428). We now report our biophysical studies establishing the nature of granzyme B-serglycin (GrB·SG) complex. Dynamic laser light scattering studies establish that SG has a hydrodynamic radius of ∼140 ± 23 nm, comparable to some viral particles. Agarose mobility shift gels and surface plasmon resonance (SPR), show that SG binds tightly to GrB and has the capacity to hold 30–60 GrB molecules. SPR studies also indicate equivalent binding affinities (K d ∼ 0.8 μm), under acidic (granule pH) and neutral isotonic conditions (extra-cytoplasmic pH), for GrB·SG interaction. Finally, characterization of GrB·SG interactions within granules revealed complexes of two distinct molecular sizes, one held ∼4–8 molecules of GrB, whereas the other contained as many as 32 molecules of GrB or other granule proteins. These studies provide a firm biophysical basis for our earlier reported observations that the proapoptotic granzyme is exocytosed predominantly as a macromolecular complex with SG.

Deamidation destabilizes and triggers aggregation of a lens protein, βA3-crystallin

Protein aggregation is a hallmark of several neurodegenerative diseases and also of cataracts. The major proteins in the lens of the eye are crystallins, which accumulate throughout life and are extensively modified. Deamidation is the major modification in the lens during aging and cataracts. Among the crystallins, the βA3‐subunit has been found to have multiple sites of deamidation associated with the insoluble proteins in vivo. Several sites were predicted to be exposed on the surface of βA3 and were investigated in this study. Deamidation was mimicked by site‐directed mutagenesis at Q42 and N54 on the N‐terminal domain, N133 and N155 on the C‐terminal domain, and N120 in the peptide connecting the domains. Deamidation altered the tertiary structure without disrupting the secondary structure or the dimer formation of βA3. Deamidations in the C‐terminal domain and in the connecting peptide decreased stability to a greater extent than deamidations in the N‐terminal domain. Deamidation at N54 and N155 also disrupted the association with the βB1‐subunit. Sedimentation velocity experiments integrated with high‐resolution analysis detected soluble aggregates at 15%–20% in all deamidated proteins, but not in wild‐type βA3. These aggregates had elevated frictional ratios, suggesting that they were elongated. The detection of aggregates in vitro strongly suggests that deamidation may contribute to protein aggregation in the lens. A potential mechanism may include decreased stability and/or altered interactions with other β‐subunits. Understanding the role of deamidation in the long‐lived crystallins has important implications in other aggregation diseases.

A locking mechanism regulates RNA synthesis and host protein interaction by the hepatitis C virus polymerase.

Mutational analysis of the hepatitis C virus (HCV) RNA-dependent RNA polymerase (RdRp) template channel identified two residues, Trp397 and His428, which are required for de novo initiation but not for extension from a primer. These two residues interact with the Δ1 loop on the surface of the RdRp. A deletion within the Δ1 loop also resulted in comparable activities. The mutant proteins exhibit increased double-stranded RNA binding compared with the wild type, suggesting that the Δ1 loop serves as a flexible locking mechanism to regulate the conformations needed for de novo initiation and for elongative RNA synthesis. A similar locking motif can be found in other viral RdRps. Products associated with the open conformation of the HCV RdRp were inhibited by interaction with the retinoblastoma protein but not cyclophilin A. Different conformations of the HCV RdRp can thus affect RNA synthesis and interaction with cellular proteins.

Domain Mapping of the Polycystin-2 C-terminal Tail Using de Novo Molecular Modeling and Biophysical Analysis

In polycystic kidney disease (PKD), polycystin-2 (PC2) is frequently mutated or truncated in the C-terminal cytoplasmic tail (PC2-C). The currently accepted model of PC2-C consists of an EF-hand motif overlapping with a short coiled coil; however, this model fails to explain the mechanisms by which PC2 truncations C-terminal to this region lead to PKD. Moreover, direct PC2 binding to inositol 1,4,5-trisphosphate receptor, KIF3A, and TRPC1 requires residues in PC2-C outside this region. To address these discrepancies and investigate the role of PC2-C in PC2 function, we performed de novo molecular modeling and biophysical analysis. De novo molecular modeling of PC2-C using the ROBETTA server predicts two domains as follows: an EF-hand motif (PC2-EF) connected by a linker to a previously unidentified C-terminal coiled coil (PC2-CC). This model differs substantially from the current model and correlates with limited proteolysis, matrix-assisted laser desorption/ionization mass spectroscopy, N-terminal sequencing, and improved coiled coil prediction algorithms. PC2-C is elongated and oligomerizes through PC2-CC, as measured by analytical ultracentrifugation and size exclusion chromatography, whereas PC2-EF is globular and monomeric. We show that PC2-C and PC2-EF have micromolar affinity for calcium (Ca2+) by isothermal titration calorimetry and undergo Ca2+-induced conformational changes by circular dichroism. Mutation of predicted EF-hand loop residues in PC2 to alanine abolishes Ca2+ binding. Our results suggest that PC2-CC is involved in PC2 oligomerization, and PC2-EF is a Ca2+-sensitive switch. PKD-associated PC2 mutations are located in regions that may disrupt these functions, providing structural insight into how PC2 mutations lead to disease.

T4 AsiA blocks DNA recognition by remodeling σ70 region 4

Bacteriophage T4 AsiA is a versatile transcription factor capable of inhibiting host gene expression as an ‘anti‐σ′ factor while simultaneously promoting gene‐specific expression of T4 middle genes in conjunction with T4 MotA. To accomplish this task, AsiA engages conserved region 4 of Eschericia coli σ70, blocking recognition of most host promoters by sequestering the DNA‐binding surface at the AsiA/σ70 interface. The three‐dimensional structure of an AsiA/region 4 complex reveals that the C‐terminal α helix of region 4 is unstructured, while four other helices adopt a completely different conformation relative to the canonical structure of unbound region 4. That AsiA induces, rather than merely stabilizes, this rearrangement can be realized by comparison to the homologous structures of region 4 solved in a variety of contexts, including the structure of Thermotoga maritima σA region 4 described herein. AsiA simultaneously occupies the surface of region 4 that ordinarily contacts core RNA polymerase (RNAP), suggesting that an AsiA‐bound σ70 may also undergo conformational changes in the context of the RNAP holoenzyme.