Protein folding: evaluation of some simple rules for the assembly of helices into tertiary structures with myoglobin as an example.
Explore the source record for details and available documents.
Amino Acid Sequence↗
SEARCH · PubMed Health
Results for “helical assembly”
Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
The mechanism of formation of inhibitor-induced ribosome helices in Entamoeba invadens.
Helices andaggregates of helices (chromatoid bodies) composed of ribosomelike particles appear in cysts and slow-growing trophozoites of Entamoeba invadens. We found that similar helix aggregates were formed abundantly in actively growing E. invadens trophozoites treated with a variety of direct or indirect inhibitors of protein synthesis. The inhibitor-induced helices appeared cytochemically and ultrastructurally identical to those seen in cysts. Numerous single helices and small arrays occurred randomly distributed throughout the trophozoite cytoplasm within 15 min after treatment with NaF, which rapidly and completely stopped all nucleic acid and protein synthesis. Cycloheximide (CH), which inhibited protein synthesis as effectively a NaF, stimulated aggregate formation more slowly, and only after a delay of 30-60 min. CH temporarily blocked NaF-stimulated aggregated formation. Aggregation was slowest with actinomycin-D, which strongly inhibited RNA synthesis but depressed protein synthesis only slowly. These results suggested that release of ribosomes from mRNA was required for aggregation. Inhibition by CH was reversible, and aggregates disappeared from CH-treated amebas shortly after they were transferred to inhibitor-free frowth medium. There was no evidence that helices assembled about a structural organizer within the cell or that the process involved metabloc activity. It was concluded that the inhibitor-induced helices were composed of mature, normally functional ribosomes and that helix formation was a spontaneous and reversible consequence of the accumulation withing the cell of free monosomes (or subunits) which were prevented from binding to mRNA.
Animals↗
Macrotubules induced by halothane: in vitro assembly.
The formation of macrotubules by the volatile anaesthetic halothane was investigated in vitro using microtubule-enriched fractions of crayfish nerve cords. Sequential studies showed that macrotubules assemble from helical ribbons of 18-20 laterally associated microtubule protofilaments which fold upon themselves to form intact macrotubules averaging 48 nm in diameter. The initial rate of macrotubule assembly is dependent on the concentration of halothane employed and is stimulated by calcium. Glycerol pretreatment blocked macrotubule formation by halothane and caused preformed macrotubules to reassemble rapidly into typical microtubules. These experiments show that microtubules and macrotubules require different conditions for assembly and support the contention that macrotubule formation by halothane is due to a direct interaction between the anaesthetic molecule and the microtubule subunit.
Animals↗
Polarization of fluorescence from single skinned glycerinated rabbit psoas fibers in rigor and relaxation.
Single skinned glycerinated muscle fibers were labelled with the fluorescent dye N-(iodoacetylamino)-1-naphthylamine-5-sulfonic acid (1,5-IAEDANS). The heavy chain of myosin (EC 3.6.1.3) was labelled predominantly when the reaction was carried out in relaxation at 0 degrees C. Mechanical properties of skinned fibers were little affected by labelling with the fluorophore. Rigor tension developed upon transferring native or labelled skinned fibers from relaxing to rigor solutions lacking Ca2+ was very small but could be enhanced by progressively incresing Ca2 concentration; the rigor tension decreased with increasing sarcomer length. Polarization of fluorescence of skinned fibers reacted with 1,5-IAEDANS was measured along the line of excitation as well as at 90 degrees to it. The mean values of parallel and perpendicular components of polarization of labelled fibers measured at 0 degrees were close to the values obtained for native fibers irrigated with 1,5-IAEDANS-labelled heavy meromyosin fiber "ghosts" irrigated with labelled heavy meromyosin, and oriented bundles of myofibrils reacted with the same fluorophore. Skinned fibers stretched above the rest length and then irrigated with 1,5-IAEDANS-labelled heavy meromyosin gave rise to polarized fluorescence close to the values theoretically predicted for an assembly of helically arranged fluorophores. Using 90 degrees detecttion system a satisfactory fit to the theory could be obtained from single fibers labelled with 1,5-IAEDANS and measured in rigor. The angle between the fiber axis and the direction of the emission dipole of 1,5-IAEDANS attached to subfragment-1 was estimated to be near 40 degrees.
Actins↗
On the sol-gel transition insolutions of kappa-carrageenan.
The disorder-order transition, which takes place at the gelpoint of k-carrageenan solutions was monitored by optical rotation and light scattering measurements. The coincidence of both sets of experimental data affords good evidence that the sol-gel transition is accompaned by a conformational change. Transition temperatures were observed to be linearly dependent on the logarthm of the salt concentration and this result is explained by the formation of double helices. Heats of gelation were measured by differential scanning calorimetry. It was found that the enthalpy increases with ionic strength, which was ascribed to the occurrence of a secondary process in which double helices are assembled into larger aggregates.
Calorimetry↗
Evolutionary and Functional Analysis of Caspase-8 and ASC Interactions to Drive Lytic Cell Death, PANoptosis.
Caspases are evolutionarily conserved proteins essential for driving cell death in development and host defense. Caspase-8, a key member of the caspase family, is implicated in nonlytic apoptosis, as well as lytic forms of cell death. Recently, caspase-8 has been identified as an integral component of PANoptosomes, multiprotein complexes formed in response to innate immune sensor activation. Several innate immune sensors can nucleate caspase-8-containing PANoptosome complexes to drive inflammatory lytic cell death, PANoptosis. However, how the evolutionarily conserved and diverse functions of caspase-8 drive PANoptosis remains unclear. To address this, we performed evolutionary, sequence, structural, and functional analyses to decode caspase-8's complex-forming abilities and its interaction with the PANoptosome adaptor ASC. Our study distinguished distinct subgroups within the death domain superfamily based on their evolutionary and functional relationships, identified homotypic traits among subfamily members, and captured key events in caspase evolution. We also identified critical residues defining the heterotypic interaction between caspase-8's death effector domain and ASC's pyrin domain, validated through cross-species analyses, dynamic simulations, and in vitro experiments. Overall, our study elucidated recent evolutionary adaptations of caspase-8 that allowed it to interact with ASC, improving our understanding of critical molecular associations in PANoptosome complex formation and the underlying PANoptotic responses in host defense and inflammation. These findings have implications for understanding mammalian immune responses and developing new therapeutic strategies for inflammatory diseases.
Caspase 8↗
Termination of procollagen chain synthesis by puromycin. Evidence that assembly and secretion require a COOH-terminal extension.
Embryonic chick fibroblasts were incubated with [14C]proline and puromycin in the low concentrations of 1 to 3 mug/ml. The molecular weight of the synthesized procollagen chains, as measured by polyacrylamide gel electrophoresis in sodium dodecyl sulfate, was progressively reduced by increasing concentrations of puromycin in this range. For example, at 3 mug/ml the great majority of the [14C]proline was contained in procollagen chains having an average molecular weight of about 95,000 instead of the control value of 125,000. Associated with this decrease in molecular weight there was a marked decrease in the incorporation of cysteine although [14C]proline incorporation was relatively unaffedted. Disulfide bond formation was drastically inhibited as was triple helix formation as measured by resistance of the procollagen to pepsin digestion. Although the shortened procollagen chains were of normal hydroxyproline content, they nevertheless were secreted much more slowly than normal procollagen. Based upon these findings, we postulate that: (a) low concentrations of puromycin terminate procollagen chains before a COOH-terminal extension is completed, (b) these COOH-terminal extensions are required for normal assembly of the three individual procollagen chains and for triple helix formation, and (c) only assembled, triple helical procollagen molecules are selected for normal secretion.
Animals↗
Mitosis and microtuble assembly.
Microtubules reconstituted in vitro are identical in helical structure with tubules making up the mitotic spindle and both are formed by a helical condensation-polymerization mechanism. The protomer of microtubules is a heterodimer (alphabeta), of mol.wt. 110000 and sedimentation coefficient, SO25,w, 6S. This dimer has one binding site for colchicine or podophyllotoxin, two sites for Vinca alkaloids, two sites for guanine nucleotides and Ca2+-binding sites. There is also a beta-chain phosphoserine. Modulation of these properties is discussed as a possible way of regulating the competence of tubulin to polymerize. Reconstituted microtubules depolymerize to a mixture of 30-36S oligomeric tubulin and 6S dimer molecules. The 30-36S tubulin appears as a ring or disc when made visible in the electron microscope by negative staining. Three pathways of microtubule assembly have been proposed involving this ring as an intermediate: (1) the uncoiling of these rings into protofilaments; (2) the stacking of rings into macrotubules; (3) the rings as a scaffold for the assembly of a short segment of microtubule helix. Finally, the regulation of mitosis is discussed in terms of recent studies of tubulin and its polymerization, and studies in vitro and in vivo of the process of mitotic-spindle formation and disassembly.
Alkaloids↗
A conserved distal-tail helical extension defines a tailspike attachment architecture in Gram-negative siphophages.
Rapid growth of bacteriophage genome collections has outpaced functional annotation of tail-tip proteins, limiting comparative analysis of host-recognition structures. Starting from a shared distal-tail gene organization in the Salmonella phages 9NA and Jersey, I developed a morphogenetic bioinformatic framework integrating gene synteny, sequence comparison, profile hidden Markov model (HMM) screening, structural evidence, structure-aware searching, and AlphaFold modeling. Comparison with the experimentally characterized lambda and Sf11 tail assemblies identified a predominantly alpha-helical C-terminal extension of the distal-tail (DT) protein associated with tailspike attachment, termed the distal-tail helical extension (DT-helix). Screening 541,986 proteins from 5167 complete NCBI RefSeq tailed-phage genomes, followed by evidence-based evaluation of sequence, genomic context, and structural architecture, identified 165 curated DT-helical-extension-associated phages. Their DT proteins segregated into six sequence groups. In the four principal multi-member groups, cognate tailspikes showed group-specific conservation in proximal N-terminal regions but substantially greater downstream diversity, consistent with sequence constraint at the DT-tailspike attachment boundary. A complementary ProstT5/Foldseek search supported the established groups but revealed no convincing additional highly divergent family. Together with the experimentally characterized Sf11 attachment interface, these findings define a recurrent morphogenetic architecture linking conserved distal-tail scaffolds to more variable receptor-binding proteins across siphophages infecting Gram-negative bacteria. Although universal exchangeability is not established, the identified scaffold-receptor-binding boundaries provide a framework for molecular characterization and rational phage engineering. Accession-level information for the 165 curated phages is available through PhageTailDB.
Viral Tail Proteins↗
Proposed knobs-into-holes packing for several membrane proteins.
We investigated the possible side chain/side chain interactions of four potential transmembrane proteins. The basic assumptions are that the proteins are alpha-helical, and that the proteins aggregate with knobs-into-holes packing. It was found that these four proteins can be assembled into stereochemically feasible bundles of alpha-helices with hydrophobic exteriors and with hydrogen bonds between the side chains of one alpha-helix and the side chains of its knobs-into-holes packed neighbors.
Bacteriophages↗
Specificity of the antibody response in inbred mice to bovine type I and type II collagen.
Mouse antibodies to soluble bovine skin (type I) collagen react with determinants which are located in the rigid triple-helical portion of the antigen and become destroyed upon unfolding the molecule. Helical antigenic determinants are dependent on the genuine chain assembly, e.g. alpha[1(I)]2alpha2. Artefactual triplehelical structures of the composition [alpha1(I)]3 or [alpha2]3 or a genetically distinct type II collagen from cartilage showed no or only weak cross-reactivity. Pepsin treatment of type I collagen known to remove short, non-helical sequences at both ends of the molecule had virtually no effect on antigenicity and immunogenic activity. A radioimmunoassay failed to detect antibodies in three congenic resistant mouse strains immunized with denatured type I collagen. These strains had been previously classified as high or low responders to native type I collagen. Agglutination titres vs denatured collagen culd already be demonstrated in nonimmune sera. The agglutinating activity was labile against heating at 56 degrees and could not be increased by immunization. Two out of five inbred strains showed a high response against pepsin-dissolved bovine type II collagen with the chain composition [alpha1(II)]3. Lack of correlation in the responder state to both collagen types indicated control by different immune response genes. Antibodies to type II collagen also reacted against triple-helical antigenic determinants and showed neglible cross-reaction with type I collagen.
Animals↗
Purification and biochemical properties of complex flagella isolated from Rhizobium lupini H13-3.
1. The complex flagella of Rhizobium lupini H13-3 differ from plain bacterial flagella in the fine structure of their filaments dominated by conspicuous helical bands, in their fragility and their resistance against heat decomposition. To elucidate the basis of these differences, the composition of complex filaments and their subunits was analysed. 2. Isolated complex flagella containing the filament and hook protions were purified by differential centrifugation. Hooks were separated by ultracentrifugation after acid degradation of filaments at pH 2. The complex filaments consist of 43 000 dalton monomers (cx-flagellin), the hooks are composed of 41 000 dalton subunits. 3. Amino acid analysis of cx-flagellin indicated the presence of approx. 417 amino acid residues. These comprise 47% hydrophobic residues and 21% Asp and Glu (or amides), but no Cys, His, Pro and Trp. No carbohydrate, phosphate or lipid moieties have been detected. Fingerprint analysis after tryptic digestion yields approx. 36 peptides, about half of them clustered in the neutral region. A comparison with the composition of varous known flagellins from plain flagella indicates a 7% higher content of hydrophobic amino acid residues in complex filaments; this is largely compensated for by the higher content of Glu and Asp (presumably as Gln and Asn) in plain filaments. 4. Immunodiffusion and immunoelectrophoresis of cx-flagellin yield single precipitin bands indicating homogeneity. In contrast, isoelectric focusing lead to three close-running bands around pH4.7. When isolated, the two major bands again produced an "isoelectric spectrum" suggesting that it reflects an allomorphism of cx-flagellin. 5. Self-assembly experiments with cx-flagellin lead to coiled fibres including helical regions, but not to intact filaments. The products resemble heat-denatured complex filaments and may represent intermediates between monomers and complete polymers.
Amino Acids↗
Evidence that the C-terminus of OprM is involved in the assembly of the VceAB-OprM efflux pump.
Although the architecture of tripartite multiple drug resistance (MDR) efflux pumps of Gram-negative bacteria has been well characterized, the means by which the components recognize each other and assemble into a functional pump remains obscure. In this study we present evidence that the C-terminal domain of the Pseudomonas aeruginosa OprM and the alpha-helical hairpin domain of Vibrio cholerae VceA play an important role in the recognition/specificity/recruitment step in the assembly of a functional, VceAB-OprM chimeric efflux pump. To our knowledge, this is the first evidence directly linking the C-terminal domain of an outer membrane efflux protein to its recruitment during the assembly of a tripartite efflux pump.
Amino Acid Sequence↗
Structure and assembly of filamentous bacterial viruses.
Filamentous bacterial viruses are flexible nucleoprotein rods, about 6 nm in diameter by 1000-2000 nm in length (depending on the virus strain). A protein shell encloses a central core of single-stranded circular DNA. The coat protein subunits forming the shell are largely alpha-helix, elongated in an axial direction, and also sloping radially, so as to overlap each other and give an arrangement of subunits reminiscent of scales on a fish. This arrangement of alpha-helices is rather like some models of myosin filaments. An early step in assembly of the virion is the formation of a complex between the viral DNA and an intracellular packaging protein that is not found in completed virions. Newly synthesized coat protein becomes associated with the plasma membrane of the cell. During the final steps of assembly, the packaging protein is displaced from the DNA and replaced by coat protein as the virion passes out through the plasma membrane of the host cell.
Bacteriophages↗
Protein-RNA interactions during TMV assembly.
A review of the structural studies of tobacco mosaic virus (TMV) is given. TMV is essentially a flat helical microcrystal with 16 1/3 subunits per turn. A single strand of RNA runs along the helix and is deeply embedded in the protein. The virus particles form oriented gels from which high-resolution X-ray fiber diffraction data can be obtained. This may be interpreted by the use of six heavy-chain derivatives to give an electron density map at 0.4 nm resolution from which the RNA configuration and the form of the inner part of the protein subunit may be determined. In addition, the protein subunits form a stable 17-fold two-layered disk which is involved in virus assembly and which crystallizes. By the use of noncrystallographic symmetry and a single heavy-atom derivative, it has been possible to solve the structure of the double disk to 0.28 nm resolution. In this structure one sees that an important structural role is played by four alpha-helices, one of which (the LR helix) appears to form the main binding site for the RNA. The main components of the binding site appear to be hydrophobic interactions with the bases, hydrogen bonds between aspartate groups and the sugars, and arginine salt bridges to the phosphate groups. The binding site is between two turns of the virus helix or between the turns of the double disk. In the disk, the region proximal to the RNA binding site is in a random coil until the RNA binds, whereupon the 24 residues involved build a well-defined structure, thereby encapsulating the RNA.
Binding Sites↗
The formation and thermal stability of in vitro assembled fibrils from acid-soluble and pepsin-treated collagens.
The role of the non-helical regions of the collagen molecule in fibrillogenesis has been investigated by comparing the kinetics of fibril formation of pepsin-treated acid-soluble collagen, acid-soluble collagen and mixtures of the two and by comparison of the thermal stabilities of the fibrils formed. The acid-soluble collagen was found to aggregate more rapidly than the pepsin-treated collagen under physiological conditions of pH and ionic strength. Variations in ionic strength, at physiological pH, were found to have differing effects on the aggregation of these two forms of soluble collagen. Fibrils formed from the pepsinized-collagen had a lower thermal stability tha n those formed from the intact collagen. The behavior observed with mixtures of acid-soluble and pepsin-treated collagens was found to be quantitatively consistent with the pepsinized collagen being able to utilize the nuclei formed by the acid-soluble collagen for subsequent growth. However, the use of the acid-soluble nuclei by the pepsinized collagen for growth did not enhance its rate of precipitation during the growth phase, nor did it enhance the thermal stability of the fibrils formed from the pepsinized collagen.
Animals↗
Macromolecular structural transitions in Pf1 filamentous bacterial virus.
The filamentous bacterial virus Pf1 is a simple model for biological filaments. We have studied the structure of the virion and report here that the helix parameters of Pf1 change sharply with temperature at about 8 degrees C. Local interactions between protein subunits change by only a few tenths of an angstrom, but the changes are amplified between one end and the other of the virion to a rotation of 15 turns and a translation of 1,000 A. The limited nature of the phase transition is probably due to the constraints of 'knobs-into-holes' interaction between side chains of adjacent alpha-helical protein subunits. Treatment of the virion with ether causes a rearrangement of protein subunits into sheets, with the alpha-helices normal to the plane of the sheet. This phase transition suggests a model for virion assembly in the bacterial membrane.
Bacteriophages↗
[Stereochemical theory of the 3-dimensional structure of globular proteins. III. Prediction of the tertiary structure].
A prediction is made of the tertiary structure of parvalbumin, the variable part of the immunoglobulin molecule, carboxypeptidase and the trypsin inhibitor. The structures obtained theoretically coincide completely with the native ones. In the case of the trypsin inhibitor molecule, the theoretical sequence of disulfide bridge formation completely coincides with the experimental data. Elements of symmetry were found in highly helical intermediate structures of the four proteins studied. The theory developed can be successfully applied for assembling the quaternary protein structure. Proceeding from this theory the mechanisms of the increased rate of assembly of protein spatial structure in conditions in vivo as compared with their assembly in vitro are analysed.
Animals↗