Stability of macromolecular complexes

Macromolecular interactions are crucial in numerous biologic processes, yet few general principles are available that establish firm expectations for the strength of these interactions or the expected contribution of specific forces. The simplest principle would be a monotonic increase in interactions as the size of the interface grows. The exact relationship might be linear or nonlinear depending on the nature of the forces involved. Simple "linear-free energy" relationships based on atomic properties have been well documented, for example, additivity for the interaction of small molecules with solvent, and, recently, have been explored for ligand-receptor interactions. Horton and Lewis propose such additivity based on buried surface area for protein-protein complexes. We investigated macromolecular interactions and found that the highest-affinity complexes do not fulfill this simple expectation. Instead, binding free energies of the tightest macromolecular complexes are roughly constant, independent of interface size, with the notable exception of DNA duplexes. By comparing these results to an earlier study of protein-ligand interactions we find that: (1) The maximum affinity is approximately 1.5 kcal/mol per nonhydrogen atom or 120 cal/mol A(2) of buried surface area, comparable to results of our earlier work; (2) the lack of an increase in affinity with interface size is likely due to nonthermodynamic factors, such as functional and evolutionary constraints rather than some fundamental physical limitation. The implication of these results have some importance for molecular design because they suggest that: (1) The stability of any given complex can be increased significantly if desired; (2) small molecule inhibitors of macromolecular interactions are feasible; and (3) different functional classes of protein-protein complexes exhibit differences in maximal stability, perhaps in response to differing evolutionary pressures. These results are consistent with the widespread observation that proteins have not evolved to maximize thermodynamic stability, but are only marginally stable.     

Quantitative experimental assessment of macromolecular crowding effects at membrane surfaces

We examined how crowding of the surfaces of lipid vesicles with either grafted polyethyleneglycol (PEG) chains or bilayer-anchored protein molecules affects the binding of soluble proteins to the vesicle surface. Escherichia coli dihydrofolate reductase (DHFR, 18 kDa) or a larger fusion protein, NusA-DHFR (72 kDa), binds reversibly but with high affinity to a methotrexate-modified lipid (MTX-PE) incorporated into large unilamellar vesicles. Incorporation of phosphatidylethanolamine-PEG5000 into the vesicles strongly decreases the affinity of binding of both proteins, to a degree that varies roughly exponentially with the lateral density of the PEG chains. Covalently coupling maltose-binding protein (MBP) to the vesicle surfaces also strongly decreases the affinity of binding of NusDHFR or DHFR, to a degree that likewise varies roughly exponentially with the surface density of anchored MBP. Surface-coupled MBP strongly decreases the rate of binding of NusDHFR to MTX-PE-incorporating vesicles but does not affect the rate of NusDHFR dissociation. The large magnitudes of these effects (easily exceeding an order of magnitude for moderate degrees of surface crowding) support previous theoretical analyses and suggest that surface-crowding effects can markedly influence a variety of important aspects of protein behavior in membranes.     

Posttranscriptional generation of macromolecular complexes

Discrete classes of mRNAs that encode functionally related proteins are associated with sequence-specific RNA-binding proteins in yeast and mammalian cells. recently reported that pre-mRNAs encoding components of inhibitory synapses are bound to neuron-specific Nova RNA-binding proteins.     

Synthesis and biological evaluation of two novel DAT-binding technetium complexes containing a piperidine based analogue of cocaine

Two new technetium complexes containing a piperidine template have been synthesized and evaluated as possible leads for the development of dopamine transporter (DAT) imaging agents. Binding data for the corresponding rhenium complexes containing either a monoaminomonoamide (MAMA') or a diaminodithiol (DADT) chelating unit exhibited significant affinity for the DAT. Initial biodistribution studies in rats revealed only a low brain uptake.     

Molecular dynamics simulations of large macromolecular complexes

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Buoyant densities of macromolecules, macromolecular complexes, and cell organelles in Nycodenz gradients

Nycodenz is a new nonionic iodinated density gradient medium which has several advantages over metrizamide. Although, overall, biological samples band at similar densities in Nycodenz and metrizamide gradients, a number of significant differences were found. As compared with metrizamide, not only does Nycodenz appear to interact less with proteins but also the buoyant density of chromatin is less affected by the amount loaded onto the gradient. A high degree of resolution is obtainable using Nycodenz gradients; thus, it is possible to separate density-labeled DNA and to subfractionate subcellular membrane fractions.     

Preparation of macromolecular complexes for cryo-electron microscopy

This protocol describes the preparation of frozen-hydrated single-particle specimens of macromolecular complexes. First, it describes how to create a grid surface coated with holey carbon by first inducing holes in a Formvar film to act as a template for the holey carbon that is stable under cryo-electron microscopy (cryo-EM) conditions and is sample-friendly. The protocol then describes the steps required to deposit the homogeneous sample on the grid and to plunge-freeze the grid into liquid ethane at the temperature of liquid nitrogen, so that it is suitable for cryo-EM visualization. It takes 4-5 h to make several hundred holey carbon grids and about 1 h to make the frozen-hydrated grids. The time required for sample purification varies from hours to days, depending on the sample and the specific procedure required. A companion protocol details how to collect cryo-EM data using an FEI Tecnai transmission electron microscope that can subsequently be processed to obtain a three-dimensional reconstruction of the macromolecular complex.     

Reversible and irreversible inhibition of phosphate transport in human erythrocytes by a membrane impermeant carbodiimide

Phosphate entry into chloride-loaded human erythrocytes is inhibited by treatment of cells with the water-soluble carbodiimide 1-ethyl-3-(4-azonia-4,4-dimethylpentyl)carbodiimide (EAC) in the absence of added nucleophile. EAC does not penetrate the erythrocyte membrane or lead to significant intermolecular cross-linking of membrane proteins. At neutral extracellular pH in chloride-free medium, only about 50% of transport is rapidly and irreversibly inhibited, but at alkaline pH, inhibition is more rapid and complete. Inhibition by EAC was reversible in the presence of extracellular NaCl. Modification of membrane sulfhydryl groups does not prevent inhibition of phosphate transport by EAC but almost complete protection is afforded by 4,4-dinitrostilbene-2,2-disulfonic acid, a reversible competitive inhibitor of anion transport. N-(4-Azido-2-nitrophenyl)-2-aminoethylsulfonate, a reversible noncompetitive inhibitor of anion transport did not protect against EAC inhibition of transport but prevented reversal of inhibition in saline medium. Transport inhibition by [3H]EAC did not lead to specific incorporation of radioactivity into Band 3, the anion transport protein. These results suggest that inhibition of anion transport by EAC is due to modification of a carboxylic acid residue in or near the transport site accessible from the external face of the membrane. The subsequent fate of the modified carboxyl residue appears to be sensitive to the orientation of the anion transport site.     

Synthesis, crystal structures and biological evaluation of water-soluble zinc complexes of zwitterionic carboxylates

Three water-soluble zinc complexes, [Zn(Cbp)₂Br₂] (1) (Cbp = N-(4-carboxybenzyl)pyridinium), {[Zn(BCbpy)₂(H₂O)₄]₃Br₆·2(BCbpy)·2(4,4′-bipy)} (2) (BCbpy = 1-(4-carboxybenzyl)-4,4′-bipyridinium) and {[Zn₄(Bpybc)₆(H₂O)₁₂](OH)₈·9H₂O}_2n (3) (Bpybc = 1,1′-bis(4-carboxybenzyl)-4,4′-bipyridinium), were synthesized and characterized by IR, elemental analysis and single-crystal X-ray crystallography. In complex 1, the central Zn atom adopts a distorted tetrahedral coordination geometry that is formed from two unidentate Cbp ligands and two Br atoms. For complex 2, the Zn atom in [Zn(BCbpy)₂(H₂O)₄]²⁺ is strongly coordinated by four water molecules and two N atoms from two BCbpy ligands, hence forming an octahedral geometry. In complex 3, each Bpybc ligand bridges two [Zn(H₂O)₃]²⁺ units through two terminal carboxylate groups in a monodentate coordination mode, thus forming a flowerlike two-dimensional network. Agarose gel electrophoresis (GE) and ethidium bromide (EB) displacement experiments indicated that complex 3 was capable of converting pBR322 DNA into open circular (OC) and linear forms, and exhibited high binding affinity toward calf-thymus DNA. MTT assay showed that complex 3 displayed inhibitory activities toward the proliferation of lung adenocarcinoma A549 and mouse sarcoma S-180 cells, with the IC₅₀ values being 27.3 and 48.8 μM, respectively.     

Synthesis and crystallographic analysis of two rhizopuspepsin inhibitor complexes.

The crystal structures of rhizopuspepsin complexed with two oligopeptide inhibitors have been determined. CP-69,799, an azahomostatine dipeptide isostere, had previously been associated with a displacement of the C-terminal subdomain of endothiapepsin [Sali, A., Veerapandian, B., Cooper, J. B., Foundling, S. I., Hoover, D. J., & Blundell, T. L. (1989) EMBO J. 8, 2179-2188]. Here, we report the measurement of two data sets, one from crystals soaked in the inhibitor and the other from protein crystallized in the presence of excess inhibitor. In neither case is there any significant movement of the C-terminal subdomain of the rhizopuspepsin. The data suggest that the energy associated with any conformational change is small and is overcome by the crystal packing forces. The second inhibitor, a hydrated difluorostatone, was examined in a search for transition-state analogs that could cast further light on the mechanism of action [Suguna, K., Padlan, E. A., Smith, C. W., Carlson, W. D., & Davies, D. R. (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 7009-7013]. The gem-diol provides a set of contact distances with the enzyme that mimic the interactions with the tetrahedral intermediate of the substrate during catalysis. These data provide support for the suggestion that the polarization of the keto group of the peptide substrate is enhanced by a hydrogen bond from the OD1 of Asp 35 (Suguna et al., 1987).     

Synthesis, X-ray crystal structure, antimicrobial activity and photodynamic effects of some thiabendazole complexes

An interesting series of metal complexes of thiabendazole (tbz) is synthesized and characterized by elemental analyses and spectroscopic studies. The crystal structure of the hydrogen bonded one dimensional Co(II) complex, namely [Co(tbz)(2)(NO(3))(H(2)O)](NO(3)) is solved by single crystal X-ray diffraction. The complex crystallizes in monoclinic space group P2(1)/a with unit cell parameters, a=14.366(2), b=11.459(4), c=15.942(3) A, beta=113.78(3) degrees and z=4. The unit cell packing reveals an extensive hydrogen bonding involving a water molecule, nitrate ligands and the protonated nitrogen atoms of the tbz ligands, resulting in a one dimensional hydrogen bonding pattern. The antimicrobial activity of the complexes against selected bacteria (Escherichia coli and Bacillus subtilis) and yeast (Aspergillus flavues) is estimated. The relationship between the enzymatic production of ROS and antimicrobial activity of the complexes is examined, and a good correlation between two factors is found. Photodynamic quantum yields of singlet oxygen production (RNO bleaching assay) and rate of superoxide generation (SOD inhibitable ferricytochrome c reduction assay and EPR spin trapping experiments using 5,5-dimethyl-1-pyrroline-N-oxide as spin trap) by the metal complexes have been studied.     

Evaluating the stoichiometry of macromolecular complexes using multisignal sedimentation velocity

Gleaning information regarding the molecular physiology of macromolecular complexes requires knowledge of their component stoichiometries. In this work, a relatively new means of analyzing sedimentation velocity (SV) data from the analytical ultracentrifuge is examined in detail. The method depends on collecting concentration profile data simultaneously using multiple signals, like Rayleigh interferometry and UV spectrophotometry. If the cosedimenting components of a complex are spectrally distinguishable, continuous sedimentation-coefficient distributions specific for each component can be calculated to reveal the molar ratio of the complex's components. When combined with the hydrodynamic information available from the SV data, a stoichiometry can be derived. Herein, the spectral properties of sedimenting species are systematically explored to arrive at a predictive test for whether a set of macromolecules can be spectrally resolved in a multisignal SV (MSSV) experiment. Also, a graphical means of experimental design and criteria to judge the success of the spectral discrimination in MSSV are introduced. A detailed example of the analysis of MSSV experiments is offered, and the possibility of deriving equilibrium association constants from MSSV analyses is explored. Finally, successful implementations of MSSV are reviewed.     

Yeast and vertebrate nuclear-pore complexes: evolutionary conserved, yet divergent macromolecular assemblies

Summary The nuclear-pore complex (NPC), which consists of ca. 50 proteins called nucleoporins, is a huge macromolecular structure that spans the nuclear envelope and is an obligatory passage for molecules in transit between the cytoplasm and the nucleus. In the last years, major progress has allowed the characterization of the so-called soluble phase of nucleocytoplasmic transport, that involves transport substrates, import and export receptors of which some belong to the karyopherin- family, and the small GTPase Ran and its modulators. In addition, the knowledge of the NPC architecture, the identification of its constituents, and the determination of the hierarchy of interactions within the pore should help to understand how nucleoporins are assembled, and how they give rise to a functional NPC through interactions with specific transport factors. In this review, we will focus on recent insights into the stationary phase of nucleocytoplasmic transport (i.e., the NPCs) that have been gained from exploiting the benefits of several organisms, such asXenopus laevis oocytes, mammalian cell lines, and the yeastSaccharomyces cerevisiae.Abbreviations FXFG phenylalanine X phenylalanine glycine - GLFG glycine leucine phenylalanine glycine - NPC nuclear-pore complex - RLNE rat liver nuclear envelope - WGA wheat germ agglutinin     

Hydrodynamic shielding of spherical subunits in macromolecular complexes

The Garcia de la Torre-Bloomfield hydrodynamic interaction tensor was used to calculate the shielding coefficient matrices for each spherical friction bead in the rigid arrays of a rod and helix. Negative values for the average shielding coefficient result for small beads adjacent to large beads, suggesting premature truncation in the series expansions employed in the hydrodynamic interaction tensor. Numerical analysis also suggests that the magnitude of geometric asymmetry is not a good measure of the extent of friction asymmetry of the molecule due to extensive hydrodynamic shielding by other subunit beads.     

Hydrodynamics of macromolecular complexes. II. Rotation

We have used the modified Oseen hydrodynamic interaction tensor along with iterative numerical solution of the coupled hydrodynamic interaction equations to calculate the rotational diffusion coefficients of macromolecular complexes composed of nonidentical spherical subunits. For the one structure, a prolate ellipsoid of revolution, for which exact solutions are available, a subunit model with the same length and volume gives asymptotic agreement with the Perrin equations. Other structures considered include plane polygonal rings, lollipops, and dumbbells.     

A simple method for freeze-drying of macromolecules and macromolecular complexes

We present a simple approach for effective freeze-drying and rotary shadowing of large molecules, molecular assemblies, and cell organelles. Simply, a suspension of specimen is adsorped to a glass coverslip, stabilized, and rinsed with 30% methanol. A second coverslip is "sandwiched" on top, and excess methanol is withdrawn from the edges then frozen by plunging into liquid nitrogen and split. Following either rotary or unidirectional shadowing and replication, the coverslip is dissolved in hydrofluoric acid. In addition to avoiding the problems encountered with air-drying specimens for rotary shadowing, the technique also reproducibly provides the thin layer of solution necessary for proper freeze-drying, regardless of how hydrophobic the sample is. The "glass sandwich" technique allows modification of the glass substrate (making it hydrophobic with carbon or hydrophilic by soaking it in alcian blue) which clearly alters the shape of macromolecular assemblies such as myosin filaments and decorated thin filaments.