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PubMed2001

Characterization of Rous sarcoma virus Gag particles assembled in vitro.

Purified retrovirus Gag proteins or Gag protein fragments are able to assemble into virus-like particles (VLPs) in vitro in the presence of RNA. We have examined the role of nucleic acid and of the NC domain in assembly of VLPs from a Rous sarcoma virus (RSV) Gag protein and have characterized these VLPs using transmission electron microscopy (TEM), scanning TEM (STEM), and cryoelectron microscopy (cryo-EM). RNAs of diverse sizes, single-stranded DNA oligonucleotides as small as 22 nucleotides, double-stranded DNA, and heparin all promoted efficient assembly. The percentages of nucleic acid by mass, in the VLPs varied from 5 to 8%. The mean mass of VLPs, as determined by STEM, was 6.5 x 10(7) Da for both RNA-containing and DNA oligonucleotide-containing particles, corresponding to a stoichiometry of about 1,200 protein molecules per VLP, slightly lower than the 1,500 Gag molecules estimated previously for infectious RSV. By cryo-EM, the VLPs showed the characteristic morphology of immature retroviruses, with discernible regions of high density corresponding to the two domains of the CA protein. In spherically averaged density distributions, the mean radial distance to the density corresponding to the C-terminal domain of CA was 33 nm, considerably smaller than that of equivalent human immunodeficiency virus type 1 particles. Deletions of the distal portion of NC, including the second Zn-binding motif, had little effect on assembly, but deletions including the charged residues between the two Zn-binding motifs abrogated assembly. Mutation of the cysteine and histidine residues in the first Zn-binding motif to alanine did not affect assembly, but mutation of the basic residues between the two Zn-binding motifs, or of the basic residues in the N-terminal portion of NC, abrogated assembly. Together, these findings establish VLPs as a good model for immature virions and establish a foundation for dissection of the interactions that lead to assembly.

Avian Sarcoma Viruses↗
PubMed2002

Reversible binding of recombinant human immunodeficiency virus type 1 gag protein to nucleic acids in virus-like particle assembly in vitro.

Recombinant human immunodeficiency virus type 1 (HIV-1) Gag protein can assemble into virus-like particles (VLPs) in suitable buffer conditions with nucleic acid. We have explored the role of nucleic acid in this assembly process. HIV-1 nucleocapsid protein, a domain of Gag, can bind to oligodeoxynucleotides with the sequence d(TG)(n) with more salt resistance than to d(A)(n) oligonucleotides. We found that assembly of VLPs on d(TG)(n) oligonucleotides was more salt resistant than assembly on d(A)(n); thus, the oligonucleotides do not simply neutralize basic residues in Gag but provide a binding surface upon which Gag molecules assemble into VLPs. We also found that Gag molecules could be "trapped" on internal d(TG)(n) sequences within 40-base oligonucleotides, rendering them unable to take part in assembly. Thus, assembly on oligonucleotides requires that Gag proteins bind near the ends of the nucleic acid, and binding of Gag to internal d(TG)(n) sequences is apparently cooperative. Finally, we showed that nucleic acids in VLPs can exchange with nucleic acids in solution; there is a hierarchy of preferences in these exchange reactions. The results are consistent with an equilibrium model of in vitro assembly and may help to explain how Gag molecules in vivo select genomic RNA despite the presence in the cell of a vast excess of cellular mRNA molecules.

Gene Products, gag↗
PubMed2002

RNA incorporation is critical for retroviral particle integrity after cell membrane assembly of Gag complexes.

The nucleocapsid (NC) domain of retroviruses plays a critical role in specific viral RNA packaging and virus assembly. RNA is thought to facilitate viral particle assembly, but the results described here with NC mutants indicate that it also plays a critical role in particle integrity. We investigated the assembly and integrity of particles produced by the human immunodeficiency virus type 1 M1-2/BR mutant virus, in which 10 of the 13 positive residues of NC have been replaced with alanines and incorporation of viral genomic RNA is virtually abolished. We found that the mutations in the basic residues of NC did not disrupt Gag assembly at the cell membrane. The mutant Gag protein can assemble efficiently at the cell membrane, and viral proteins are detected outside the cell as efficiently as they are for the wild type. However, only approximately 10% of the Gag molecules present in the supernatant of this mutant sediment at the correct density for a retroviral particle. The reduction of positive charge in the NC basic domain of the M1-2/BR virus adversely affects both the specific and nonspecific RNA binding properties of NC, and thus the assembled Gag polyprotein does not bind significant amounts of viral or cellular RNA. We found a direct correlation between the percentage of Gag associated with sedimented particles and the amount of incorporated RNA. We conclude that RNA binding by Gag, whether the RNA is viral or not, is critical to retroviral particle integrity after cell membrane assembly and is less important for Gag-Gag interactions during particle assembly and release.

Amino Acid Substitution↗
PubMed2002

Structural requirements for the assembly of Norwalk virus-like particles.

Norwalk virus (NV) is the prototype strain of a group of human caliciviruses responsible for epidemic outbreaks of acute gastroenteritis. While these viruses do not grow in tissue culture cells or animal models, expression of the capsid protein in insect cells results in the self-assembly of recombinant NV virus-like particles (rNV VLPs) that are morphologically and antigenically similar to native NV. The X-ray structure of the rNV VLPs has revealed that the capsid protein folds into two principal domains: a shell (S) domain and a protruding (P) domain (B. V. V. Prasad, M. E. Hardy, T. Dokland, J. Bella, M. G. Rossmann, and M. K. Estes, Science 286:287-290, 1999). To investigate the structural requirements for the assembly of rNV VLPs, we performed mutational analyses of the capsid protein. We examined the ability of 10 deletion mutants of the capsid protein to assemble into VLPs in insect cell cultures. Deletion of the N-terminal 20 residues, suggested by the X-ray structure to be involved in a switching mechanism during assembly, did not affect the ability of the mutant capsid protein to self-assemble into 38-nm VLPs with a T=3 icosahedral symmetry. Further deletions in the N-terminal region affected particle assembly. Deletions in the C-terminal regions of the P domain, involved in the interactions between the P and S domains, did not block the assembly process, but they affected the size and stability of the particles. Mutants carrying three internal deletion mutations in the P domain, involved in maintaining dimeric interactions, produced significantly larger 45-nm particles, albeit in low yields. The complete removal of the protruding domain resulted in the formation of smooth particles with a diameter that is slightly smaller than the 30-nm diameter expected from the rNV structure. These studies indicate that the shell domain of the NV capsid protein contains everything required to initiate the assembly of the capsid, whereas the entire protruding domain contributes to the increased stability of the capsid by adding intermolecular contacts between the dimeric subunits and may control the size of the capsid.

Animals↗
PubMed1996

Drosophila NAP-1 is a core histone chaperone that functions in ATP-facilitated assembly of regularly spaced nucleosomal arrays.

We describe the cloning and analysis of Drosophila nucleosome assembly protein 1 (dNAP-1), a core histone-binding protein that functions with other chromatin assembly activities in a Drosophila chromatin assembly factor 1-containing fraction (dCAF-1 fraction) in the ATP-facilitated assembly of regularly spaced nucleosomal arrays from purified core histones and DNA. Purified, recombinant dNAP-1 acts cooperatively with a factor(s) in the dCAF-1 fraction in the efficient and DNA replication-independent assembly of chromatin. In the presence of histone H1, the repeat length of the chromatin is similar to that of native chromatin from Drosophila embryos. By coimmunoprecipitation analysis, dNAP-1 was found to be associated with histones H2A and H2B in a crude whole-embryo extract, which suggests that dNAP-1 is bound to the histones in vivo. Studies of the localization of dNAP-1 in the Drosophila embryo revealed that the factor is present in the nucleus during S phase and is predominantly cytoplasmic during G2 phase. These data suggest that NAP-1 acts as a core histone shuttle which delivers the histones from the cytoplasm to the chromatin assembly machinery in the nucleus. Thus, NAP-1 appears to be one component of a multifactor chromatin assembly machinery that mediates the ATP-facilitated assembly of regularly spaced nucleosomal arrays.

Adenosine Triphosphate↗
PubMed1996

Microtubule assembly competence analysis of freshly-biopsied human tau, dephosphorylated tau, and Alzheimer tau.

Phosphorylation of the microtubule-associated protein tau regulates its binding to microtubules; highly phosphorylated tau is also a prime component of paired helical filaments (PHFs) of Alzheimer's disease (AD). Tau from freshly biopsied human, monkey, and rat brain share similar electrophoretic mobility patterns and overlapping phosphorylated epitopes when compared to AD tau isolated from AD brain. We compared the microtubule reassembly competence of fresh isolates of phosphorylated tau to that of maximally dephosphorylated tau and tau from AD brain. A rapid procedure was developed which permitted the enrichment of phosphorylated and dephosphorylated tau from human biopsies in the absence of protein kinase and phosphatase activity. Microtubule assembly assays, using a spectrophotometric measure and purified bovine brain tubulin, were used to correlate assembly competence with states of tau electrophoretic mobility. Maximally dephosphorylated human biopsy-derived tau and monkey tau were assembly competent; tau from AD brain was virtually unable to direct microtubule assembly. Unmodified, biopsy-derived tau from non-AD brain was intermediate in assembly competence relative to AD tau and dephosphorylated tau. Several lines of evidence were used to correlate phosphorylation states of tau with microtubule assembly. First, in vitro dephosphorylation of human biopsy-derived tau with either PP2A or PP2B alone or in combination led to increasing assembly competence as the electrophoretic mobility of tau increased. Second, addition of the protein phosphatase inhibitor okadaic acid (10 microM) to brain-slice preparations slowed electrophoretic mobility of tau and decreased binding competence. We suggest that tau derived from freshly-biopsied brain exists in a range of phosphorylated states, and that dephosphorylation by PP2A and/or PP2B increases microtubule assembly competence.

Alzheimer Disease↗
PubMed2000

Time-lapse confocal reflection microscopy of collagen fibrillogenesis and extracellular matrix assembly in vitro.

The development of the next generation of biomaterials for restoration of tissues and organs (i.e., tissue engineering) requires a better understanding of the extracellular matrix (ECM) and its interaction with cells. Extracellular matrix is a macromolecular assembly of natural biopolymers including collagens, glycosaminoglycans (GAGs), proteoglycans (PGs), and glycoproteins. Interestingly, several ECM components have the ability to form three-dimensional (3D), supramolecular matrices (scaffolds) in vitro by a process of self-directed polymerization, "self-assembly". It has been shown previously that 3D matrices with distinct architectural and biological properties can be formed from either purified type I collagen or a complex mixture of interstitial ECM components derived from intestinal submucosa. Unfortunately, many of the imaging and analysis techniques available to study these matrices either are unable to provide insight into 3D preparations or demand efforts that are often prohibitory to observations of living, dynamic systems. This is the first report on the use of reflection imaging at rapid time intervals combined with laser-scanning confocal microscopy for analysis of structural properties and kinetics of collagen and ECM assembly in 3D. We compared time-lapse confocal reflection microscopy (TL-CRM) with a well-established spectrophotometric method for determining the self-assembly properties of both purified type I collagen and soluble interstitial ECM. While both TL-CRM and spectrophotometric techniques provided insight into the kinetics of the polymerization process, only TL-CRM allowed qualitative and quantitative evaluation of the structural parameters (e.g., fibril diameter) and 3D organization (e.g., fibril density) of component fibrils over time. Matrices formed from the complex mixture of soluble interstitial ECM components showed an increased rate of assembly, decreased opacity, decreased fibril diameter, and increased fibril density compared to that of purified type I collagen. These results suggested that the PG/GAG components of soluble interstitial ECM were affecting the polymerization of the component collagens. Therefore, the effects of purified and complex mixtures of PG/GAG components on the assembly properties of type I collagen and interstitial ECM were evaluated. The data confirmed that the presence of PG/GAG components altered the kinetics and the 3D fibril morphology of assembled matrices. In summary, TL-CRM was demonstrated to be a new and useful technique for analysis of the 3D assembly properties of collagen and other natural biopolymers which requires no specimen fixation and/or staining.

Animals↗
PubMed2002

Diastereoselective noncovalent synthesis of hydrogen-bonded double-rosette assemblies.

Chiral centers present either in the dimelamine components of calix[4]arene 1 or in the cyanurate components CA quantitatively induce one handedness (P or M) in the corresponding hydrogen-bonded assemblies 1(3).(CA)(6) (de>98 %). The high degree of chiral induction results from the presence of six chiral centers in close proximity (C(alpha)) to the core of the assembly. A much lower level of chiral induction is observed for assemblies with chiral centers that are more remote (C(beta)). All diastereomerically pure assemblies 1(3).(CA)(6) exhibit very high CD activities (deltavarepsilon(max) approximately 100 L mol(-1) cm(-1)), in sharp contrast to the low CD activities (deltavarepsilon(max)<or=8 L mol(-1) cm(-1)) shown by the free components. The assemblies display spontaneous resolution under thermodynamically controlled conditions (i.e., heteromeric assemblies containing both peripheral R and S centers are not observed. Remarkable assembly behavior is observed if both components 1 and CA are chiral. In general, formation of well-defined assemblies is only observed when both components contain unidirectional information for the induction of either M or P chirality.

Journal Article↗
PubMed2003

A molecular approach to self-assembly of trimethylsilylacetylene derivatives on gold.

We recently discovered that a linear multifunctional trimethylsilylacetylene (TMSA) compound forms long-range and highly stable self-assembled monolayers (SAMs) on reconstructed Au(111). To better understand the interactions governing self-assembly in this new system, we synthesized a series of homologue organosilanes and performed scanning tunneling microscopy (STM) measurements at the Au(111)/n-tetradecane interface. The four TMSA-terminated linear silanes that we synthesized self-assemble in similar ways on gold, with the molecules standing upright on the surface. In contrast, compounds with a slightly modified terminal group but the same polyunsaturated linear chain above the TMSA head do not self-assemble. In particular, substituting a methyl group of TMSA with a more bulky one prevents self-assembly. Removing the C triple bond C triple bond of TMSA or substituting the Si atom by a C atom also hinders self-assembly. Finally, substituting one methyl group of TMSA by a hydrogen atom induces self-assembly but in a different geometry, with the molecules lying flat on the gold surface in a quasi-epitaxy mode. Our molecular approach demonstrates the key role played by the TMSA head in self-assembly, its origin being twofold: 1) the TMSA layers are commensurate to the Au(111) adlattice along the <112> direction, and 2) the C triple bond C triple bond of TMSA activates the Si atom and induces the creation of a surface Si-Au chemical bond. The highly stable TMSA-based SAMs appear then as promising materials for applications in surface modification.

Journal Article↗
PubMed2006

Naturally engineered glycolipid biosurfactants leading to distinctive self-assembled structures.

Self-assembling properties of "natural" glycolipid biosurfactants, mannosyl-erythritol lipids A and B (MEL-A, MEL-B), which are abundantly produced from yeast strains, were investigated by using the fluorescence-probe method, dynamic light-scattering (DLS) analysis, freeze-fracture transmission electron microscopy (FF-TEM), and synchrotron small/wide-angle X-ray scattering (SAXS/WAXS) analysis, among other methods. Both MEL-A and MEL-B exhibit excellent self-assembly properties at extremely low concentrations; they self-assemble into large unilamellar vesicles (LUV) just above their critical-aggregation concentration (CAC). The CAC(I) value was found to be 4.0x10(-6) M for MEL-A and 6.0x10(-6) M for MEL-B. Moreover, the self-assembled structure of MEL-A above a CAC(II) value of 2.0x10(-5) M was found to drastically change into sponge structures (L3) composed of a network of randomly connected bilayers that are usually obtained from a complicated multicomponent "synthetic" surfactant system. Interestingly, the average water-channel diameter of the sponge structure was 100 nm. This is relatively large compared with those obtained from "synthetic" surfactant systems. In addition, MEL-B, which has a hydroxyl group at the C-4' position on mannose instead of an acetyl group, gives only one CAC; the self-assembled structure of MEL-B seems to gradually move from LUV to multilamellar vesicles (MLV) with lattice constants of 4.4 nm, depending on the concentration. Furthermore, the lyotropic-liquid-crystal-phase observation at high concentrations demonstrates the formation of an inverted hexagonal phase (H2) for MEL-A, together with a lamella phase (L(alpha)) for MEL-B, indicating a difference between MEL-A and MEL-B molecules in the spontaneous curvature of the assemblies. These results clearly show that the difference in spontaneous curvature caused by the single acetyl group on the head group probably decides the direction of self-assembly of glycolipid biosurfactants. The unique and complex molecular structures with several chiral centers that are molecularly engineered by microorganisms must have led to the sophisticated self-assembling properties of the glycolipid biosurfactants.

Chemistry Techniques, Analytical↗
PubMed1995

Desmosome assembly and disassembly are regulated by reversible protein phosphorylation in cultured epithelial cells.

Desmosomes are one component of the intercellular junctional complex in epithelia. In cultures of epithelial cells, desmosome assembly can be regulated by modulating the calcium concentrations of the growth media. At present, very little is known about the intracellular signal transduction mechanisms that regulate desmosome assembly and disassembly in response to changing extracellular calcium concentrations. We have used inhibitors of protein kinases and phosphatases in a combined biochemical and morphological approach to analyze the role of protein phosphorylation in the assembly and disassembly of desmosomes in Madin-Darby canine kidney epithelial cells. Our results suggest that desmosomal proteins (desmoplakins I/II and desmoglein 1) are primarily phosphorylated on serine residues. Electron microscopic analyses of desmosome assembly upon induction of cell-cell contact, in the presence of protein kinase inhibitor, H-7, revealed an apparently normal assembly of desmosomes. However, complete disassembly of desmosomes was inhibited by H-7 upon removal of extracellular calcium. Under these conditions, although desmosomes split, desmosomal plaques and their associated cytokeratin filaments can not be internalized. In contrast, treatment of the cultures with okadaic acid (OA), an inhibitor of protein phosphatases, inhibited desmosome assembly but had no effect on disassembly. In addition, the inhibitory effect of okadaic acid on desmosome assembly was specific to this junction since we observed apparently normal tight junction and adherens junction in okadaic acid-treated cultures. These results suggest that assembly and disassembly of desmosomes may be regulated by extracellular Ca2+ via reversible protein phosphorylation involving both protein kinase and protein phosphatases.

1-(5-Isoquinolinesulfonyl)-2-Methylpiperazine↗
PubMed1986

Site-specific disruption of clathrin assembly produces novel structures.

Clathrin assembly in vitro produces a highly ordered polyhedral structure (basket). This resembles clathrin assembled in situ on coated pits and vesicles which form during receptor-mediated endocytosis. Sites on clathrin involved in assembly were identified by assembling clathrin in the presence of anti-clathrin monoclonal antibodies. Three of the antibodies, as IgG, prevented the assembly of normal baskets, and their Fab fragments induced formation of two types of novel clathrin structures. Antibody effects on assembly and competitive binding data indicate these antibodies bind to two sites, critical for clathrin interactions, located in the same region of the clathrin heavy chain. Analysis of novel structures formed, suggested that nucleation but not further assembly was occurring, implying an ordered sequence of clathrin interactions during assembly.

Animals↗
PubMed2006

Site-directed combinatorial construction of chimaeric genes: general method for optimizing assembly of gene fragments.

Site-directed construction of chimaeric genes by in vitro recombination "mixes-and-matches" precise building blocks from multiple parent proteins, generating libraries of hybrids to be tested for structure-function relationships and/or screened for favorable properties and novel enzymatic activities. A direct annealing and ligation method can construct chimaeric genes without requiring sequence identity between parents, except for the short (approximately 3 nt) sequences of the fragment overhangs used for specific ligation. Careful planning of the assembly process is necessary, though, in order to ensure effective construction of desired fragment assemblies and to avoid undesired assemblies (e.g., repetition of fragments, fragments out of order). We develop algorithms for specific planned ligation of short overhangs (SPLISO) that efficiently explore possible assembly plans, varying the fragment overhangs and the order of ligation steps in the assembly pathway. While there is a combinatorial explosion in the number of possible assembly plans as the number of breakpoints and parent genes increases, we employ a dynamic programming approach to find globally optimal ones in low-order polynomial time (in practice, taking only seconds for basic assembly plans). We demonstrate the effectiveness of our algorithms in planning the assembly of hybrid libraries, under a variety of experimental options and restrictions, including flexibility in the position and amino acid sequence of breakpoints. Our method promises to enable more effective application of site-directed recombination to protein investigation and engineering.

Algorithms↗
PubMed1999

The effects of mono-ADP-ribosylation on desmin assembly-disassembly.

Previous studies have shown that desmin, the muscle-specific intermediate filament protein, is a substrate for the endogenous muscle arginine-specific mono-ADP-ribosyltransferase and that ADP-ribosylation inhibits assembly of desmin into intermediate filaments (Huang et al., Exp. Cell Res. 226, 147-153, 1996). In this paper, the effects of mono-ADP-ribosylation on assembly and disassembly of desmin intermediate filaments were further characterized. First, it was found that ADP-ribosylated desmin does not coassemble with unmodified desmin and has no effect on assembly of unmodified desmin. Second, incubation of assembled desmin filaments with mono-ADP-ribosyltransferase and NAD+ results in disassembly of the filaments. Finally, the structural components of the attached ADP-ribose moiety responsible for altering the assembly of desmin into filaments were investigated by a stepwise cleavage of ADP-ribose with snake venom phosphodiesterase and alkaline phophatase, followed by analysis of assembly. The reactions catalyzed by these two enzymes were established using a desmin peptide as a substrate. Our results show that ribosylated desmin, but not phosphoribosylated desmin, was able to self-assemble into intermediate filaments, suggesting that the presence of a phosphate group is needed to alter desmin's assembly ability.

ADP Ribose Transferases↗
PubMed1999

DNA molecules can drive the assembly of other DNA molecules into specific four-stranded structures.

Single-stranded DNA molecules containing clustered G-repeats can be assembled into various four-stranded structures linked by G-quartets. Here, we report that such molecules can also drive the assembly of other DNA molecules containing G-repeats into specific four-stranded structures. In these assays, the oligonucleotides 5'-CAGGCTGAGCAGGTACGGGGGAGCTGGGGTAGATTGGAATGTAG-3' (oligo D) and 5'-CGGGGGAGCTGGGGT-3' (oligo B), consisting of sequences found in immunoglobulin switch regions, were annealed in a buffer containing K+ and the annealing products were analyzed by polyacrylamide gel electrophoresis. This analysis revealed that whereas annealing of each oligo alone produced four-stranded structures designated D2 and B2, annealing of mixtures containing both oligos produced additional complexes designated D2* and B2*. D2* and B2* were found to contain only D molecules and only B molecules, respectively. The yield of D2* increased and the yield of B2* decreased, as the concentration ratio oligo B/oligo D was increased. These results indicated that B can drive the assembly of D into D2* and D can drive the assembly of B into B2*. Further studies revealed that while the assembly of D2 followed a second order kinetics, the B-driven assembly of D2* followed a first order kinetics. Dimethyl sulfate footprinting indicated that both D2 and D2* are four-stranded structures containing two parallel and two antiparallel chains. In addition, annealing of D mixed with various B mutants showed that only mutants containing two G-clusters can drive the assembly of D2*. Based on these data, we propose that in the process of D2* assembly, a four-stranded intermediate containing B and D is formed and then dissociates into D2* and B in a rate-limiting first order reaction. Driver mechanisms of this type may cause formation of specific four-stranded structures at G-rich chromosomal sites, thereby regulating processes such as recombination and telomere synthesis.

Base Sequence↗
PubMed1999

Effect of antibiotics on large ribosomal subunit assembly reveals possible function of 5 S rRNA.

Functional large ribosomal subunits of Thermus aquaticus can be reconstituted from ribosomal proteins and either natural or in vitro transcribed 23 S and 5 S rRNA. Omission of 5 S rRNA during subunit reconstitution results in dramatic decrease of the peptidyl transferase activity of the assembled subunits. However, the presence of some ribosome-targeted antibiotics of the macrolide, ketolide or streptogramin B groups during 50 S subunit reconstitution can partly restore the activity of ribosomal subunits assembled without 5 S rRNA. Among tested antibiotics, macrolide RU69874 was the most active: activity of the subunits assembled in the absence of 5 S rRNA was increased more than 30-fold if antibiotic was present during reconstitution procedure. Activity of the subunits assembled with 5 S rRNA was also slightly stimulated by RU69874, but to a much lesser extent, approximately 1.5-fold. Activity of the native T. aquaticus 50 S subunits incubated in the reconstitution conditions in the presence of RU69874 was, in contrast, slightly decreased. The presence of antibiotics was essential during the last incubation step of the in vitro assembly, indicating that drugs affect one of the last assembly steps. The 5 S rRNA was previously shown to form contacts with segments of domains II and V of 23 S rRNA. All the antibiotics which can functionally compensate for the lack of 5 S rRNA during subunit reconstitution interact simultaneously with the central loop in domain V (which is known to be a component of peptidyl transferase center) and a loop of the helix 35 in domain II of 23 S rRNA. It is proposed that simultaneous interaction of 5 S rRNA or of antibiotics with the two domains of 23 S rRNA is essential for the successful assembly of ribosomal peptidyl transferase center. Consequently, one of the functions of 5 S rRNA in the ribosome can be that of assisting the assembly of ribosomal peptidyl transferase by correctly positioning functionally important segments of domains II and V of 23 S rRNA.

Anti-Bacterial Agents↗
PubMed2000

Bacteriophage T4 gene 59 helicase assembly protein binds replication fork DNA. The 1.45 A resolution crystal structure reveals a novel alpha-helical two-domain fold.

The bacteriophage T4 gene 59 helicase assembly protein is required for recombination-dependent DNA replication, which is the predominant mode of DNA replication in the late stage of T4 infection. T4 gene 59 helicase assembly protein accelerates the loading of the T4 gene 41 helicase during DNA synthesis by the T4 replication system in vitro. T4 gene 59 helicase assembly protein binds to both T4 gene 41 helicase and T4 gene 32 single-stranded DNA binding protein, and to single and double-stranded DNA. We show here that T4 gene 59 helicase assembly protein binds most tightly to fork DNA substrates, with either single or almost entirely double-stranded arms. Our studies suggest that the helicase assembly protein is responsible for loading T4 gene 41 helicase specifically at replication forks, and that its binding sites for each arm must hold more than six, but not more than 12 nucleotides. The 1.45 A resolution crystal structure of the full-length 217-residue monomeric T4 gene 59 helicase assembly protein reveals a novel alpha-helical bundle fold with two domains of similar size. Surface residues are predominantly basic (pI 9.37) with clusters of acidic residues but exposed hydrophobic residues suggest sites for potential contact with DNA and with other protein molecules. The N-terminal domain has structural similarity to the double-stranded DNA binding domain of rat HMG1A. We propose a speculative model of how the T4 gene 59 helicase assembly protein might bind to fork DNA based on the similarity to HMG1, the location of the basic and hydrophobic regions, and the site size of the fork arms needed for tight fork DNA binding. The fork-binding model suggests putative binding sites for the T4 gene 32 single-stranded DNA binding protein and for the hexameric T4 gene 41 helicase assembly.

Amino Acid Sequence↗
PubMed2001

Protein-dependent transition states for ribonucleoprotein assembly.

Native folding and splicing by the Saccharomyces cerevisiae mitochondrial bI5 group I intron RNA is facilitated by both the S. cerevisiae CBP2 and Neurospora crassa CYT-18 protein cofactors. Both protein-bI5 RNA complexes splice at similar rates, suggesting that the RNA active site structure is similar in both ribonucleoproteins. In contrast, the two proteins assemble with the bI5 RNA by distinct mechanisms and bind opposing, but partially overlapping, sides of the group I intron catalytic core. Assembly with CBP2 is limited by a slow, unimolecular RNA folding step characterized by a negligible activation enthalpy. We show that assembly with CYT-18 shows four distinctive features. (1) CYT-18 binds stably to the bI5 RNA at the diffusion controlled limit, but assembly to a catalytically active RNA structure is still limited by RNA folding, as visualized directly using time-resolved footprinting. (2) This mechanism of rapid stable protein binding followed by subsequent assembly steps has a distinctive kinetic signature: the apparent ratio of k(off) to k(on), determined in a partitioning experiment, differs from the equilibrium K(d) by a large factor. (3) Assembly with CYT-18 is characterized by a large activation enthalpy, consistent with a rate limiting conformational rearrangement. (4) Because assembly from the kinetically trapped state is faster at elevated temperature, we can identify conditions where CYT-18 accelerates (catalyzes) bI5 RNA folding relative to assembly with CBP2.

Allosteric Site↗