Components Of Multiprotein Complexes Research Articles

Histone Deacetylase Co-Repressor Complex Control of Runx2 and Bone Formation

A decade has passed since the transcription factor, Runx2, was found to be essential for osteoblast development and chondrocyte hypertrophy. During the last 10 years, our understanding of Runx2's physiological roles and the molecular mechanisms whereby it regulates gene expression to control cell-cycle progression and cellular differentiation has increased exponentially. Runx2 is expressed in osteoblasts, prehypertrophic chondrocytes, mesenchymal cells of the perichondrium, T lymphocytes, endothelial cells, and breast and prostate epithelial cells, with increased expression observed in breast and prostate carcinomas. Although Runx2 and other mammalian Runt domain proteins were originally described as transcriptional activators, they are also transcriptional repressors and thus maintain functional similarities with their Drosophila homolog, Runt. Runx2 binds a consensus DNA sequence but does not possess any enzymatic activities that directly affect chromatin structure. It alters gene expression by recruiting cofactors to gene regulatory elements. Histone deacetylases (HDACs) are among the co-repressors that interact with Runx2. In this review, we summarize data demonstrating that several HDACs and their associated proteins interact with Runx2, regulate its activity, and affect bone formation. HDACs are components of multiprotein complexes that interact with many transcription factors and are subject to regulation by extracellular signals. The elucidation of HDAC complex components that influence Runx2 activity in specific cell types and in response to various extracellular stimuli will increase our understanding of how this crucial transcription factor functions, and how we might be able to control its activity to influence bone formation or reduce bone disease associated with cancer metastasis.

A novel random mutagenesis method and the incorporation of an isotopic label into a protein

There are limitations on the current methods used to diversify protein sequences, such as the inability to scan mutations throughout an entire protein. We have developed a novel method, “Codon Scanning Mutagenesis”, which allows for rapid and complete scanning of a protein sequence with the use of elementary molecular biology techniques. This method is made possible by a modified transposon mutagenesis approach that randomly targets DNA sequences. This transposon allows for random insertion of a NotI restriction site, which is unique to the DNA sequence to be mutated. The randomized insertion of this restriction site thus allows for the insertion of a linker with strategically placed type II restriction sites. The properties of the type II restriction sites allow for a codon to be replaced with a new codon. We are specifically interested in the random insertion of TAG stop codons which code for unnatural amino acids carrying photoaffinity labels that can be used to probe protein-protein interactions. Finally, we show that the detection of photo-crosslinked protein-protein interactions can easily be done by mass spectrometry studies when the deuterated p-benzoylphenylalanine is incorporated as an isotopic label. This method will allow for obtaining structural information on multi-component protein complexes, provide insight into the active site residues, or even trap receptor ligands at the cell surface.

Crystallography of complexes

The CCP4 Study Weekend 2006 covered a wide range of topics associated with structural studies of complexes between proteins, proteins and nucleic acids and proteins and small molecules. The programme was composed of lectures from different areas of structural biology including: preparation and characterization of complexes for structural analysis, co-crystallization and soaking techniques, molecular replacement with multiple protein components, and fitting and refinement of small-molecule ligands. However, the underlying theme of the presentations was about those aspects of macromolecular crystallography which are specific to the determination of crystal structures of molecular ensemblies, undertaken to throw light on biological processes or reveal molecular interactions between protein targets and potential drug molecules. The meeting, held at the University of Leeds, attracted the highest number of participants (over 550) in the history of these popular annual gatherings, which clearly showed that the topics presented in the lectures were seen as relevant to the research activities of a large number of structural biologists from different areas. As usual, the talks were focused on methods rather than the final results of authors’ research for the benefit of a large number of students and young scientists in the audience. The first day of the meeting was devoted to the methods and techniques specific to the studies of complexes between macromolecules. The importance of such studies for better understanding of biology at the molecular level was illustrated by excellent talks by Joel Janin and Michael Rossmann in the opening session called Biology is Molecular Interactions. The subsequent presentations by Tim Dafforn and John Ladbury described methods of preparation of macromolecular complexes for structure determination and techniques to study the formation of such complexes in solution, prior to crystallisation attempts, using a variety of biochemical and biophysical approaches including dynamic light scattering (DLS), ultracentrifugation and isothermal titration calorimetry (ITC). The final session of the day included talks on the application of molecular replacement methods to multi-component protein complexes (Airlie McCoy), modelling of high-resolution structures into medium-resolution electron-microscopy maps (Ruth Nussinov) and on computational analysis of surface complementarity in macromolecular complexes (Martin Noble). Structural studies of the interactions between macromolecules and small ligands were the subject of the lectures on the second day of the meeting. First, an introduction to the geometry of small molecules, linked to their chemical properties, was presented by Phil Evans and set the scene for a number of later talks on the modelling and refinement of such molecules, bound to their protein targets. Several presentations in the first two sessions of the day, given by speakers from pharmaceutical companies, covered a wide spectrum of methodologies applied to facilitate the crystallographic analysis of protein-small molecule interactions. Biophysical methods to detect formation of protein–small molecule ligand complexes in solution prior to co-crystallization experiments were described by Chun-wa Chung, followed by a presentation by Annie Hassell of a large number of standard and non-standard techniques and tricks used to create well diffracting crystals of complexes with potential drugs. An overview of the impact structural biology had on the design of new leukaemia drugs, presented by Sandra Jacob, convincingly illustrated the role macromolecular crystallography of complexes plays in the discovery of new medicines. The last session of the meeting included talks on the different approaches used to fit small molecules into corresponding electron density and refine them using appropriate geometrical restraints (Tom Terwilliger and Victor Lamzin). In the same session, Gerard Kleywegt once more emphasised the importance of using the right sets of geometry descriptors for the ligands in both model building and refinement.

Quantitative proteomic analysis of distinct mammalian Mediator complexes using normalized spectral abundance factors

Components of multiprotein complexes are routinely determined by using proteomic approaches. However, this information lacks functional content except when new complex members are identified. To analyze quantitatively the abundance of proteins in human Mediator we used normalized spectral abundance factors generated from shotgun proteomics data sets. With this approach we define a common core of mammalian Mediator subunits shared by alternative forms that variably associate with the kinase module and RNA polymerase (pol) II. Although each version of affinity-purified Mediator contained some kinase module and RNA pol II, Mediator purified through F-Med26 contained the most RNA pol II and the least kinase module as demonstrated by the normalized spectral abundance factor approach. The distinct forms of Mediator were functionally characterized by using a transcriptional activity assay, where F-Med26 Mediator/RNA pol II was the most active. This method of protein complex visualization has important implications for the analysis of multiprotein complexes and assembly of protein interaction networks.

Probing Genuine Strong Interactions and Post-translational Modifications in the Heterogeneous Yeast Exosome Protein Complex

The characterization of heterogeneous multicomponent protein complexes, which goes beyond identification of protein subunits, is a challenging task. Here we describe and apply a comprehensive method that combines a mild affinity purification procedure with a multiplexed mass spectrometry approach for the in-depth characterization of the exosome complex from Saccharomyces cerevisiae expressed at physiologically relevant levels. The exosome is an ensemble of primarily 3' --> 5' exoribonucleases and plays a major role in RNA metabolism. The complex has been reported to consist of 11 proteins in molecular mass ranging from 20 to 120 kDa. By using native macromolecular mass spectrometry we measured accurate masses (around 400 kDa) of several (sub)exosome complexes. Combination of these data with proteolytic peptide LC tandem mass spectrometry using a linear ion trap coupled to a FT-ICR mass spectrometer and intact protein LC mass spectrometry provided us with the identity of the different exosome components and (sub)complexes, including the subunit stoichiometry. We hypothesize that the observed complexes provide information about strongly and weakly interacting exosome-associated proteins. In our analysis we also identified for the first time phosphorylation sites in seven different exosome subunits. The phosphorylation site in the Rrp4 subunit is fully conserved in the human homologue of Rrp4, which is the only previously reported phosphorylation site in any of the human exosome proteins. The described multiplexed mass spectrometry-based procedure is generic and thus applicable to many different types of cellular molecular machineries even if they are expressed at endogenous levels.

The Dynamin-like Protein Vps1p of the Yeast Saccharomyces cerevisiae Associates with Peroxisomes in a Pex19p-dependent Manner

Dynamins and dynamin-like proteins play important roles in organelle division. In Saccharomyces cerevisiae, the dynamin-like protein Vps1p (vacuolar protein sorting protein 1) is involved in peroxisome fission, as cells deleted for the VPS1 gene contain reduced numbers of enlarged peroxisomes. What relationship Vps1p has with peroxisomes remains unclear. Here we show that Vps1p interacts with Pex19p, a peroxin that acts as a shuttling receptor for peroxisomal membrane proteins or as a chaperone assisting the assembly/stabilization of proteins at the peroxisome membrane. Vps1p contains two putative Pex19p recognition sequences at amino acids 509-523 and 633-647. Deletion of the first (but not the second) sequence results in reduced numbers of enlarged peroxisomes in cells, as in vps1delta cells. Deletion of either sequence has no effect on vacuolar morphology or vacuolar protein sorting, suggesting that the peroxisome and vacuole biogenic functions of Vps1p are separate and separable. Substitution of proline for valine at position 516 of Vps1p abrogates Pex19p binding and gives the peroxisome phenotype of vps1delta cells. Microscopic analysis showed that overexpression of Pex19p or redirection of Pex19p to the nucleus does not affect the normal cellular distribution of Vps1p in the cytosol and in punctate structures that are not peroxisomes, suggesting that Pex19p does not function in targeting Vps1p to peroxisomes. Subcellular fractionation showed that a fraction of Vps1p is associated with peroxisomes and that deletion or mutation of the first Pex19p recognition sequence abrogates this association. Our results are consistent with Pex19p acting as a chaperone to stabilize the association of Vps1p with peroxisomes and not as a receptor involved in targeting Vps1p to peroxisomes.

Measuring the Elasticity of Clathrin-Coated Vesicles via Atomic Force Microscopy

Using a new scheme based on atomic force microscopy (AFM), we investigate mechanical properties of clathrin-coated vesicles (CCVs). CCVs are multicomponent protein and lipid complexes of ∼100 nm diameter that are implicated in many essential cell-trafficking processes. Our AFM imaging resolves clathrin lattice polygons and provides height deformation in quantitative response to AFM-substrate compression force. We model CCVs as multilayered elastic spherical shells and, from AFM measurements, estimate their bending rigidity to be 285 ± 30 k B T, i.e., ∼20 times that of either the outer clathrin cage or inner vesicle membrane. Further analysis reveals a flexible coupling between the clathrin coat and the membrane, a structural property whose modulation may affect vesicle biogenesis and cellular function.

Identification by mass spectrometry and functional characterization of two phosphorylation sites of KCNQ2/KCNQ3 channels

Neuronal potassium channel subunits of the KCNQ (Kv7) family underlie M-current (I(M)), and may also underlie the slow potassium current at the node of Ranvier, I(Ks). I(M) and I(Ks) are outwardly rectifying currents that regulate excitability of neurons and myelinated axons, respectively. Studies of native I(M) and heterologously expressed Kv7 subunits suggest that, in vivo, KCNQ channels exist within heterogeneous, multicomponent protein complexes. KCNQ channel properties are regulated by protein phosphorylation, protein-protein interactions, and protein-lipid interactions within such complexes. To better understand the regulation of neuronal KCNQ channels, we searched directly for posttranslational modifications on KCNQ2/KCNQ3 channels in vivo by using mass spectrometry. Here we describe two sites of phosphorylation. One site, specific for KCNQ3, appears functionally silent in electrophysiological assays but is located in a domain previously shown to be important for subunit tetramerization. Mutagenesis and electrophysiological studies of the second site, located in the S4-S5 intracellular loop of all KCNQ subunits, reveal a mechanism of channel inhibition.

Isotopically Coded Cleavable Cross-linker for Studying Protein-Protein Interaction and Protein Complexes

An emerging approach for studying protein-protein interaction in complexes is the combination of chemical cross-linking and mass spectrometric analysis of the cross-linked peptides (cross-links) obtained after proteolysis of the complex. This approach, however, has several challenges and limitations, including the difficulty of detecting the cross-links, the potential interference from non-informative "cross-linked peptides" (dead end and intrapeptide cross-links), and unambiguous identification of the cross-links by mass spectrometry. Thus, we have synthesized an isotopically coded ethylene glycol bis(succinimidylsuccinate) derivate (D12-EGS), which contains 12 deuterium atoms for easy detection of cross-links when applied in a 1:1 mixture with its H12 counterpart and is also cleavable for releasing the cross-linked peptides allowing unambiguous identification by MS sequencing. Moreover, hydrolytic cleavage permits rapid distinguishing between different types of cross-links. Cleavage of a dead end cross-link produces a doublet with peaks 4.03 Da apart, with the lower peak appearing at a molecular mass 162 Da lower than the mass of the H12 form of the original cross-linked peptide. Cleavage of an intrapeptide cross-link leads to a doublet 8.05 Da apart and 62 Da lower than the molecular mass of the H12 form of the original cross-linked peptide. Cleavage of an interpeptide cross-link forms a pair of 4.03-Da doublets, with the lower mass member of each pair each shifted up from its unmodified molecular weight by 82 Da because of the attached portion of the cross-linker. All of this information has been incorporated into a software algorithm allowing automatic screening and detection of cross-links and cross-link types in matrix-assisted laser desorption/ionization mass spectra. In summary, the ease of detection of these species through the use of an isotopically coded cleavable cross-linker and our software algorithm, followed by mass spectrometric sequencing of the cross-linked peptides after cleavage, has been shown to be a powerful tool for studies of multi-component protein complexes.

Binding of HTm4 to Cyclin-dependent Kinase (Cdk)-associated Phosphatase (KAP)·Cdk2·Cyclin A Complex Enhances the Phosphatase Activity of KAP, Dissociates Cyclin A, and Facilitates KAP Dephosphorylation of Cdk2

Cyclin-dependent kinase 2 (cdk2) activation requires phosphorylation of Thr160 and dissociation from cyclin A. The T-loop of cdk2 contains a regulatory phosphorylation site at Thr160. An interaction between cdc-associated phosphatase (KAP) and cdk2 compromises the interaction between cdk2 and cyclin A, which permits access of KAP, a Thr160-directed phosphatase, to its substrate, cdk2. We have reported that KAP is bound and activated by a nuclear membrane protein, HTm4. Here, we present in vitro data showing the direct interaction between the HTm4 C terminus and KAP Tyr141. We show that this interaction not only facilitates access of KAP to Thr160 and accelerates KAP kinetics, but also forces exclusion of cyclin A from the KAP.cdk2 complex.

Multi-Component Protein Complexes and Golgi Membrane Trafficking

Several large cytosolic protein complexes with multiple components have been proposed to play key roles in mediating or controlling membrane trafficking. Among these complexes, TRAPP, COG and GARP/VFT have been implicated in multiple steps of Golgi membrane trafficking. The importance of these complexes for Golgi function has been established using in vitro biochemical assays and yeast and mammalian somatic cell genetics. Furthermore, mutations in the genes encoding subunits of either TRAPP or the COG complex have been shown to be responsible for human genetic disorders. We here review recent studies exploring the structures and functions of these three oligomeric complexes.

Evidence for specific tetraspanin homodimers: inhibition of palmitoylation makes cysteine residues available for cross-linking.

It is a well-established fact that tetraspanin proteins, a large family of integral membrane proteins involved in cell motility, fusion and signalling, associate extensively with one another and with other transmembrane and membrane-proximal proteins. In this study, we present results strongly suggesting that tetraspanin homodimers are fundamental units within larger tetraspanin complexes. Evidence for constitutive CD9 homodimers was obtained using several cell lines, utilizing the following four methods: (1) spontaneous cross-linking via intermolecular disulphide bonds, (2) use of a cysteine-reactive covalent cross-linking agent, (3) use of an amino-reactive covalent cross-linking agent, and (4) covalent cross-linking via direct intermolecular disulphide bridging between unpalmitoylated membrane-proximal cysteine residues. In the last case, incubation of cells with the palmitoylation inhibitor 2-bromopalmitate exposed membrane-proximal cysteine residues, thus effectively promoting 'zero-length' cross-linking to stabilize homodimers. Similar to CD9, other tetraspanins (CD81 and CD151) also showed a tendency to homodimerize. Tetraspanin homodimers were assembled from newly synthesized proteins in the Golgi, as evidenced by cycloheximide and Brefeldin A inhibition studies. Importantly, tetraspanin homodimers appeared on the cell surface and participated in typical 'tetraspanin web' interactions with other proteins. Whereas homodimers were the predominant cross-linked species, we also observed some higher-order complexes (trimers, tetramers or higher) and a much lower level of cross-linking between different tetraspanins (CD81-CD9, CD9-CD151, CD81-CD151). In conclusion, our results strongly suggest that tetraspanin homodimers, formed in the Golgi and present at the cell surface, serve as building blocks for the assembly of larger, multicomponent tetraspanin protein complexes.

Transcriptional regulation of protein complexes in yeast.

Multiprotein complexes play an essential role in many cellular processes. But our knowledge of the mechanism of their formation, regulation and lifetimes is very limited. We investigated transcriptional regulation of protein complexes in yeast using two approaches. First, known regulons, manually curated or identified by genome-wide screens, were mapped onto the components of multiprotein complexes. The complexes comprised manually curated ones and those characterized by high-throughput analyses. Second, putative regulatory sequence motifs were identified in the upstream regions of the genes involved in individual complexes and regulons were predicted on the basis of these motifs. Only a very small fraction of the analyzed complexes (5-6%) have subsets of their components mapping onto known regulons. Likewise, regulatory motifs are detected in only about 8-15% of the complexes, and in those, about half of the components are on average part of predicted regulons. In the manually curated complexes, the so-called 'permanent' assemblies have a larger fraction of their components belonging to putative regulons than 'transient' complexes. For the noisier set of complexes identified by high-throughput screens, valuable insights are obtained into the function and regulation of individual genes. A small fraction of the known multiprotein complexes in yeast seems to have at least a subset of their components co-regulated on the transcriptional level. Preliminary analysis of the regulatory motifs for these components suggests that the corresponding genes are likely to be co-regulated either together or in smaller subgroups, indicating that transcriptionally regulated modules might exist within complexes.

DNA replication: a complex matter.

In eukaryotic cells, the essential function of DNA replication is carried out by a network of enzymes and proteins, which work together to rapidly and accurately duplicate the genetic information of the cell. Many of the components of this DNA replication apparatus associate with other cellular factors as components of multiprotein complexes, which act cooperatively in networks to regulate cell cycle progression and checkpoint control, but are distinct from the pre-replication complexes that associate with the origins and regulate their firing. In this review, we summarize current knowledge about the composition and dynamics of these large multiprotein complexes in mammalian cells and their relationships to the replication factories.

Overproduction and analysis of eukaryotic multiprotein complexes in Escherichia coli using a dual-vector strategy

Biochemical studies of eukaryotic proteins are often constrained by low availability of these typically large, multicomponent protein complexes in pure form. Escherichia coli is a commonly used host for large-scale protein production; however, its utility for eukaryotic protein production is limited because of problems associated with transcription, translation, and proper folding of proteins. Here we describe the development and testing of pLANT, a vector that addresses many of these problems simultaneously. The pLANT vector contains a T7 promoter-controlled expression unit, a p15A origin of replication, and genes for rare transfer RNAs and kanamycin resistance. Thus, the pLANT vector can be used in combination with the pET vector to coexpress multiple proteins in E. coli. Using this approach, we have successfully produced high-milligram quantities of two different Saccharomyces cerevisiae complexes in E. coli: the heterodimeric Msh2–Msh6 mismatch repair protein (248 kDa) and the five-subunit replication factor C clamp loader (250 kDa). Quantitative analyses indicate that these proteins are fully active, affirming the utility of pLANT+pET-based production of eukaryotic proteins in E. coli for in vitro studies of their structure and function.

γ-Secretase Activity Is Associated with a Conformational Change of Nicastrin

Gamma-secretase is a high molecular weight multicomponent protein complex with an unusual intramembrane-cleaving aspartyl protease activity. Gamma-secretase is intimately associated with Alzheimer disease because it catalyzes the proteolytic cleavage, which leads to the liberation of amyloid beta-peptide. At least presenilin (PS), Nicastrin (Nct), APH-1, and PEN-2 are constituents of the gamma-secretase complex, with PS apparently providing the active site of gamma-secretase. Expression of gamma-secretase complex components is tightly regulated, however little is known about the assembly of the complex. Here we demonstrate that Nct undergoes a major conformational change during the assembly of the gamma-secretase complex. The conformational change is directly associated with gamma-secretase function and involves the entire Nct ectodomain. Loss of function mutations generated by deletions failed to undergo the conformational change. Furthermore, the conformational alteration did not occur in the absence of PS. Our data thus suggest that gamma-secretase function critically depends on the structural "activation" of Nct.

Studying the assembly of multicomponent protein and ribonucleoprotein complexes using surface plasmon resonance

The assembly of large macromolecular complexes is an important aspect of cellular organization and metabolism. Interactions involving such complexes in principle follow the same rules as the interactions between single proteins or other macromolecules and can therefore be investigated using similar approaches. We have developed protocols employing standard surface plasmon resonance technology that allow the investigation of interactions involving complex macromolecular structures. The principal experimental challenges arise from the possibility of parallel reactions where partially assembled or dissociated subcomplexes form a significant proportion of the molecule population and from an increased likelihood of unspecific binding events owing to the larger surface and statistically higher number of charged areas on multisubunit assemblies. Ways to experimentally avoid or, where this is not possible, to control for these complications are discussed.

Mechanism of antibiotic efflux in Gram-negative bacteria.

Active efflux of antibiotics mediated by multidrug transporters is a mechanistic basis of multidrug resistance in bacteria. The most versatile multidrug transporters are those found in Gram-negative bacteria. They have a high level of constitutive expression and provide an immediate response to structurally diverse antimicrobial agents including clinically important antibiotics. The versatility and efficiency of multidrug transporters in Gram-negative bacteria heavily depend on coupling of drug efflux with the transport across the outer membrane. The coupling is achieved through the assembly of multi-component protein complexes that span both the inner and the outer membranes of Gram-negative bacteria. In this review we discuss the mechanistic and structural features of multidrug efflux complexes with the major focus on the tight coupling of drug efflux with transport across the outer membrane.

Protein- and immunoaffinity purification of multiprotein complexes

This chapter discusses the protein and immunoaffinity purification of multiprotein complexes. Virtually all proteins must interact with other proteins to carry out their activities within the cell. Protein affinity chromatography allows the exploitation of this fundamental property to identify proteins that function together as components of multiprotein complexes. The chapter discusses two methods for identifying interacting proteins by affinity chromatography. In the first method, a protein affinity column is made by linking relatively large amounts of a purified protein to a column matrix. A crude extract is then passed over the column and specifically bound proteins are eluted with a buffer containing high salt or denaturants, such as urea. In the second approach, endogenous protein complexes are purified using an immunoaffinity column made by linking antibodies that recognize a specific protein to a column matrix. The chapter discusses the in vitro protein interactions that are relevant in vivo.

Lentinula edodes produces a multicomponent protein complex containing manganese (II)-dependent peroxidase, laccase and β-glucosidase

A multicomponent protein complex containing manganese (II)-dependent peroxidase, laccase and β-glucosidase was isolated from culture extracts of the white rot basidiomycete Lentinula edodes. This protein complex showed a single protein band on native polyacrylamide gel electrophoresis (PAGE). On sodium dodecyl sulfate (SDS)–PAGE, however, it displayed three major bands and several additional minor bands ranging in size from 60 kDa to 180 kDa, suggesting it being a complex of six to eight different proteins. The molecular mass of this complex was estimated to be approximately 660 kDa from the elution position of gel filtration. This enzyme complex was effective in transforming environmentally persistent xenobiotics, pentachlorophenol and 2,5-dichlorophenol.