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Assembly of recombinant human immunodeficiency virus type 1 capsid protein in vitro.

The capsid protein (CA) (p24) of human immunodeficiency virus (HIV) type 1 expressed in Escherichia coli and purified to greater than 90% homogeneity was used to examine assembly in vitro and to probe the nature of interactions involved in the formation of capsid structures. The protein was detected in dimeric and oligomeric forms as indicated by molecular size measurements by gel filtration column chromatography, sedimentation through sucrose, and nondenaturing gel electrophoresis. Chemical cross-linking of CA molecules was observed with several homobifunctional reagents. Oligomer size was dependent on cross-linker concentration and exhibited a nonrandom pattern in which dimers and tetramers were more abundant than trimers and pentamers. Oligomers as large as dodecamers were detected in native polyacrylamide gels. These were stable in solutions of high ionic strength or in the presence of nonionic detergent, indicating that strong interactions were involved in oligomer stabilization. Limited tryptic digestion converted the putative dodecamers to octamers, suggesting that a region involved in CA protein multimerization was exposed in the structure. This region was mapped to the central portion of the protein. The recombinant CA proteins assembled in vitro into long rodlike structures and were disassembled into small irregular spheres by alterations in ionic strength and pH. The observation that assembly and disassembly of purified HIV type 1 CA protein can be induced in vitro suggests an approach for identifying possible control mechanisms involved in HIV viral core assembly.

Capsid↗

Molecular organization of Mason-Pfizer monkey virus capsids assembled from Gag polyprotein in Escherichia coli.

We describe the results of a study by electron microscopy and image processing of Gag protein shells-immature capsids--of Mason-Pfizer monkey virus assembled in Escherichia coli from two truncated forms of the Gag precursor: Deltap4Gag, in which the C-terminal p4Gag was deleted, and Pro(-)CA.NC, in which the N-terminal peptides and proline 1 of the CA domain were deleted. Negative staining of capsids revealed small patches of holes forming a trigonal or hexagonal pattern most clearly visible on occasional tubular forms. The center-to-center spacing of holes in the network was 7.1 nm in Deltap4Gag capsids and 7.4 nm in Pro(-)CA.NC capsids. Image processing of Deltap4Gag tubes revealed a hexagonal network of holes formed by six subunits with a single subunit shared between rings. This organization suggests that the six subunits are contributed by three trimers of the truncated Gag precursor. Similar molecular organization was observed in negatively stained Pro(-)CA.NC capsids. Shadowed replicas of freeze-etched capsids produced by either construct confirmed the presence of a hexagonal network of holes with a similar center-to-center spacing. We conclude that the basic building block of the cage-like network is a trimer of the Deltap4Gag or Pro(-)CA.NC domains. In addition, our results point to a key role of structurally constrained CA domain in the trimeric interaction of the Gag polyprotein.

Animals↗

Crystallization and identification of an assembly defect of recombinant antenna complexes produced in transgenic tobacco plants.

A chimeric Lhcb gene encoding light-harvesting chlorophyll a/b-binding protein (LHCII) was expressed in transgenic tobacco plants. To separate native from recombinant LHCII, the protein was extended by six histidines at its C terminus. Recombinant LHCII was isolated by detergent-mediated monomerization of pure trimers followed by affinity-chromatography on Ni(2+)-NTA-agarose (NTA is nitrilotriacetic acid). Elution with imidazole yielded recombinant monomers that formed trimers readily after dilution of the detergent without further in vitro manipulations. LHCII subunits showed the typical chlorophyll a/b ratio at all steps of purification indicating no significant loss of pigments. Transgenic tobacco overexpressed amounts of recombinant protein that corresponded to about 0.7% of total LHCII. This yield suggested that expression in planta might be an alternative to the expression of eukaryotic membrane proteins in yeast. Recombinant LHCII was able to form two-dimensional crystals after addition of digalactolipids, which diffracted electrons to 3.6-A resolution. LHCII carrying a replacement of Arg-21 with Gln accumulated to only 0.004% of total thylakoid proteins. This mutant was monomeric in the photosynthetic membrane probably due to the deletion of the phosphatidylglycerol binding site and was degraded by the plastidic proteolytic system. Exchange of Asn-183 with Leu impaired LHCII biogenesis in a similar way presumably due to the lack of a chlorophyll a binding site.

Arabidopsis Proteins↗

Trimeric ring-like structure of ArsA ATPase.

ArsA protein is the soluble subunit of the Ars anion pump in the Escherichia coli membrane which extrudes arsenite or antimonite from the cytoplasm. The molecular weight of the subunit is 63 kDa. In the cell it hydrolyzes ATP, and the energy released is used by the membrane-bound subunit ArsB to transport the substrates across the membrane. We have obtained two-dimensional crystals of ArsA in the presence of arsenite on negatively-charged lipid monolayer composed of DMPS and DOPC. These crystals have been studied using electron microscopy of negatively-stained specimens followed by image processing. The projection map obtained at 2.4 nm resolution reveals a ring-like structure with threefold symmetry. Many molecular assemblies with the same ring-shape and dimensions were also seen dispersed on electron microscopy grids, prepared directly from purified ArsA protein solution. Size-exclusion chromatography of the protein sample with arsenite present revealed that the majority of the protein particles in solution have a molecular weight of about 180 kDa. Based on these experiments, we conclude that in solution the ArsA ATPase with substrate bound is mainly in a trimeric form.

Adenosine Triphosphatases↗

tert-Butylphosphonic acid: from the bulk to the gas phase.

The structure of tert-butylphosphonic acid in the solid, in solution, and in the gas phase was studied by single-crystal X-ray diffraction, (1)H and (31)P NMR spectroscopic studies in solution, solid-state (31)P NMR spectroscopy, and electrospray ionization mass spectrometry. In addition, density functional theory (DFT) calculations at the B3LYP/6-31G*, B3LYP/6-31+G*, and B3LYP/6-311+G* level of theory for a large number of H-bonded aggregates of the type (tBuPO(3)H(2))(n) (C(n), P(n); n=1-7) support the experimental work. Crystallization of tBuPO(3)H(2) from polar solvents such as CH(3)CN or THF gives the H-bonded one-dimensional polymer 2, whereas crystallization from the less polar solvent CDCl(3) favors the formation of the H-bonded cluster (tBuPO(3)H(2))(6).CDCl(3) (1). In CDCl(3) the hexamer (tBuPO(3)H(2))(6) (C(6)) is replaced by smaller aggregates down to the monomer with decreasing concentration. DFT calculations and natural bond orbital (NBO) analyses for the clusters C(1)-C(7) and the linear arrays P(1)-P(7) reveal the hexamer C(6) to be the energetically favored structure resulting from cooperative strengthening of the hydrogen bonds in the H-bonded framework. However, the average hydrogen bond strengths calculated for C(6) and P(2) do not differ significantly (42-43 kJ mol(-1)). The average distances r(O.O), r(Obond;H), r(Pdbond;O), and r(Pbond;OH) in C(1)-C(7) and P(1)-P(7) are closely related to the hydrogen bond strength. Electrospray ionization mass spectrometry shows the presence of different anionic species of the type [(tBuPO(3)H(2))(n)-H](-) (A(1)-A(7), n=1-7) depending on the instrumental conditions. DFT calculations at the B3LYP/6-31G* level of theory were carried out for A(1)-A(6). We suggest the dimer [(tBuPO(3)H(2))(2)-H](-) (A(2)) and the trimer [(tBuPO(3)H(2))(3)-H](-) (A(3)) are the energetically favored anionic structures. A hydrogen bond energy of approximately 83 kJ mol(-1) was calculated for A(2). Electrospray ionization mass spectrometry is not suitable to study the assembling process of neutral H-bonded tert-butylphosphonic acid since the removal of a proton from the neutral aggregates has a large influence on the hydrogen bond strength and the cluster structure.

Journal Article↗

Synthesis and structural characterization of a novel mixed-valent Cu(II)Cu(I)Cu(II) triangular metallomacrocycle using an imine-based rigid ligand.

A novel neutral mixed-valent Cu(I)Cu(II)(2) triangular metallomacrocycle [Cu(3)L(2)(HL)].3CH(3)OH.2H(2)O (1) was assembled by reaction of the tetradentate ligand bis(N-salicylidene-4,4'-diphenylamine), H(2)L, with a copper(II) salt. ESI-MS show peaks only corresponding to the triangular structural species, indicating the high stability of the trimer structure in solution. Magnetic study confirms that there are two Cu(II) ions and one Cu(I) ion in a discrete triangular molecule. The crystal structure of 1 reveals that the triangle is formed by three deprotonated ligands and three copper ions with a Cu-Cu separation of ca. 11.8 A. Each copper atom is coordinated by two oxygen atoms and two nitrogen atoms from two different bis-bidentate ligands in a heavily distorted tetrahedral geometry, while each ligand is bound to two metal ions in a bis-bidentate coordination mode and links the metal centers overlapping in an unprogressive manner. Strong intramolecular pi.pi interactions between the ligands are found to stabilize the constraint conformation of the triangle. Electrochemical study reveals that the mixed-valent Cu(I)Cu(II)(2) complex is the most stable state in solution condition, and the electrochemical communication between the copper ions might be explained on the basis of the through-bond interaction. UV-vis-NIR spectral measurement demonstrates the Robin-Day class II behavior of the mixed-valence compound with a weak copper-copper interaction.

Journal Article↗

Crystal structure of NC1 domains. Structural basis for type IV collagen assembly in basement membranes.

Type IV collagen, which is present in all metazoan, exists as a family of six homologous alpha(IV) chains, alpha1-alpha6, in mammals. The six chains assemble into three different triple helical protomers and self-associate as three distinct networks. The network underlies all epithelia as a component of basement membranes, which play important roles in cell adhesion, growth, differentiation, tissue repair and molecular ultrafiltration. The specificity of both protomer and network assembly is governed by amino acid sequences of the C-terminal noncollagenous (NC1) domain of each chain. In this study, the structural basis for protomer and network assembly was investigated by determining the crystal structure of the ubiquitous [(alpha1)(2).alpha2](2) NC1 hexamer of bovine lens capsule basement membrane at 2.0 A resolution. The NC1 monomer folds into a novel tertiary structure. The (alpha1)(2).alpha2 trimer is organized through the unique three-dimensional domain swapping interactions. The differences in the primary sequences of the hypervariable region manifest in different secondary structures, which determine the chain specificity at the monomer-monomer interfaces. The trimer-trimer interface is stabilized by the extensive hydrophobic and hydrophilic interactions without a need for disulfide cross-linking.

Amino Acid Sequence↗

Transport of the IgE receptor alpha-chain is controlled by a multicomponent intracellular retention signal.

The human high affinity IgE receptor (FcepsilonRI) is a central component of the allergic response and is expressed as either a trimeric alphagamma2 or tetrameric alphabetagamma2 complex. It has been previously described that the cytoplasmic domain (CD) of the alpha-chain carries a dilysine motif at positions -3/-7 from the C terminus that functions in intracellular retention prior to assembly with other FcepsilonRI subunits. In this report we have further explored the role of the -3/-7 dilysine signal in controlling steady-state alpha-chain transport by mutational analysis and found little surface expression of a -3/-7 dialanine alpha-chain mutant but significant Golgi localization. We compared the transport properties of a series of alpha-chain cytoplasmic domain truncation mutants and observed that truncation mutants lacking 23 or more C-terminal residues showed a dramatic increase in steady-state transport suggesting a role for the membrane-proximal CD sequence in alpha-chain retention. By performing alanine-scanning mutagenesis we identified a dilysine sequence (Lys(212)-Lys(216)) proximal to the transmembrane domain (TMD) that is important for both alpha-chain cell-surface expression and intracellular stability. Furthermore, co-mutation of the Lys(212)-Lys(216) residues with the -3/-7 dilysine signal produced a dramatic increase in alpha-chain surface expression that was further increased by co-mutation of the lone charged residue (Asp(192)) in the TMD thereby defining three regions that function to regulate alpha-chain transport and in a highly synergistic manner.

Alanine↗

Structural and evolutionary inference from molecular variation in Neisseria porins.

The porin proteins of the pathogenic Neisseria species, Neisseria gonorrhoeae and Neisseria meningitidis, are important as serotyping antigens, putative vaccine components, and for their proposed role in the intracellular colonization of humans. A three-dimensional structural homology model for Neisseria porins was generated from Escherichia coli porin structures and N. meningitidis PorA and PorB sequences. The Neisseria sequences were readily assembled into the 16-strand beta-barrel fold characteristic of porins, despite relatively low sequence identity with the Escherichia proteins. The model provided information on the spatial relationships of variable regions of peptide sequences in the PorA and PorB trimers and insights relevant to the use of these proteins in vaccines. The nucleotide sequences of the porin genes from a number of other Neisseria species were obtained by PCR direct sequencing and from GenBank. Alignment and analysis of all available Neisseria porin sequences by use of the structurally conserved regions derived from the PorA and PorB structural models resulted in the recovery of an improved phylogenetic signal. Phylogenetic analyses were consistent with an important role for horizontal genetic exchange in the emergence of different porin classes and confirmed the close evolutionary relationships of the porins from N. meningitidis, N. gonorrhoeae, Neisseria lactamica, and Neisseria polysaccharea. Only members of this group contained three conserved lysine residues which form a potential GTP binding site implicated in pathogenesis. The model placed these residues on the inside of the pore, in close proximity, consistent with their role in regulating pore function when inserted into host cells.

Amino Acid Sequence↗

Supramolecular architecture of severe acute respiratory syndrome coronavirus revealed by electron cryomicroscopy.

Coronavirus particles are enveloped and pleomorphic and are thus refractory to crystallization and symmetry-assisted reconstruction. A novel methodology of single-particle image analysis was applied to selected virus features to obtain a detailed model of the oligomeric state and spatial relationships among viral structural proteins. Two-dimensional images of the S, M, and N structural proteins of severe acute respiratory syndrome coronavirus and two other coronaviruses were refined to a resolution of approximately 4 nm. Proteins near the viral membrane were arranged in overlapping lattices surrounding a disordered core. Trimeric glycoprotein spikes were in register with four underlying ribonucleoprotein densities. However, the spikes were dispensable for ribonucleoprotein lattice formation. The ribonucleoprotein particles displayed coiled shapes when released from the viral membrane. Our results contribute to the understanding of the assembly pathway used by coronaviruses and other pleomorphic viruses and provide the first detailed view of coronavirus ultrastructure.

Cryoelectron Microscopy↗

FAS death domain deletions and cellular FADD-like interleukin 1beta converting enzyme inhibitory protein (long) overexpression: alternative mechanisms for deregulating the extrinsic apoptotic pathway in diffuse large B-cell lymphoma subtypes.

PURPOSE: Large B-cell lymphomas (LBCL) arise from normal antigen-exposed B cells at germinal center (GC) or post-GC stages of differentiation. Negative selection of normal low-affinity or self-reactive GC B-cells depends on CD95 (FAS)-mediated apoptosis. FAS mutations that result in deletion of the cytoplasmic death domain destabilize the trimeric receptor and inhibit FAS-mediated apoptosis. This apoptotic pathway is also inhibited when the nuclear factor kappaB (NFkappaB) target, cellular FADD-like interleukin 1beta converting enzyme inhibitory protein (cFLIP), interacts with the death-inducing signaling complex, assembled around the FAS death domain. Herein, we ask whether FAS death domain mutations and NFkappaB-mediated overexpression of cFLIP represent alternative mechanisms for deregulating the extrinsic apoptotic pathway in LBCL subtypes defined by gene expression profiling [oxidative phosphorylation, B-cell receptor/proliferation, and host response diffuse LBCLs and primary mediastinal LBCLs]. EXPERIMENTAL DESIGN: The FAS receptor was sequenced, FAS death domain mutations identified, and cFLIP expression assessed in a series of primary LBCLs with gene expression profiling-defined subtype designations and additional genetic analyses [t(14;18) and t(3;v)]. RESULTS: FAS death domain deletions were significantly more common in oxidative phosphorylation tumors, which also have more frequent t(14;18), implicating structural abnormalities of either the extrinsic or intrinsic pathway in this diffuse LBCL subtype. In marked contrast, host response tumors, which have up-regulation of multiple NFkappaB target genes and increased NFkappaB activity, express significantly higher levels of cFLIP(long). CONCLUSIONS: These data suggest that the gene expression profiling-defined LBCL subtypes have different mechanisms for deregulating FAS-mediated cell death and, more generally, that these tumor groups differ with respect to their underlying genetic abnormalities.

Apoptosis↗

Cuticular collagen synthesis by Ascaris suum during development from the third to fourth larval stage: identification of a potential chemotherapeutic agent with a novel mechanism of action.

The dominant proteins released by Ascaris suum during development in vitro from the L3 to L4 stage were identified as collagenous cuticular proteins by sequence analysis and susceptibility to digestion by collagenase. Under reducing sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), the collagen proteins separated into 3 groups with molecular weights estimated at 32 kDa, 54-60 kDa, and 71-91 kDa. The 32-kDa protein represents monomeric collagen; the 54-60- and 71-91-kDa components represent dimeric and trimeric forms, respectively, polymerized by nonreducible cross-links. Furthermore, the release of these forms of collagen was developmentally regulated, as exemplified by a sequential temporal progression from monomeric to dimeric to trimeric forms in association with the in vitro transition from L3 to L4. The data suggest that collagen released in vitro during development of A. suum L3 to L4 reflects the increased translation of collagen gene products and their initial assembly into higher molecular weight molecules associated with the synthesis of the L4 cuticle. A biotinylated dipeptidyl fluoromethylketone cysteine protease inhibitor (Bio-phe-ala-FMK) bound specifically to the 32-kDa collagen and, to a lesser extent, to a 30-kDa protein; binding was dependent on the presence of dithiothreitol (DTT) and was prevented by iodoacetamide. Because cysteine residues play an essential role in the initial assembly of the collagen monomers into the higher molecular weight oligomers present in the mature nematode cuticle, inhibition of molting of A. suum L3 to L4 by the cysteine protease inhibitor Z-phe-ala-FMK might be due to its binding to thiol groups of collagen monomers during a critical phase of collagen assembly. Prevention of cystine cross-links during this critical period of cuticle assembly by peptide-FMK inhibitors may represent a potential control mechanism having a novel mechanism of action.

Amino Acid Sequence↗

Direct, solid phase assembly of dihydropyrroloindole peptides with conjugated oligonucleotides.

A new controlled pore glass (CPG) support is described that allows for the direct synthesis of oligonucleotide derivatives carrying a minor groove binding (MGB) agent at the 3'-terminus. The MGB consisted of three repeating 1,2-dihydro-3H-pyrrolo[2,3-e]indole-7-carboxylate (DPI) subunits. The DPI trimer (DPI3) was prepared directly on the CPG support using repeated addition of the DPI subunit. The subunit was protected at the N-3-position with tert-butyloxycarbonyl residue and activated at the 7-carboxy residue by esterification with the 2,3,5,6-tetrafluorophenyl group. A linker, which provided the starting point for oligonucleotide synthesis, was introduced by reaction of the terminal N-3 with p-nitrophenyl 4-[bis(4-methoxyphenyl)phenylmethoxy]butyrate. When used as a support for oligonucleotide synthesis, this modified CPG gave the desired 3'-DPI3-octathymidylate [(dTp)8-DPI3] conjugate in good yield. This conjugate formed hyperstabilized complexes with complementary polyribo- (Tmax = 35 degrees C) and polydeoxyriboadenylic (Tmax = 69 degrees C) acids. In contrast to the N-carbamoyl derivative reported earlier by us, it demonstrated higher cooperativity of melting transitions.

Glass↗

Nucleation and growth phases in the polymerization of coat and scaffolding subunits into icosahedral procapsid shells.

The polymerization of protein subunits into precursor shells empty of DNA is a critical process in the assembly of double-stranded DNA viruses. For the well-characterized icosahedral procapsid of phage P22, coat and scaffolding protein subunits do not assemble separately but, upon mixing, copolymerize into double-shelled procapsids in vitro. The polymerization reaction displays the characteristics of a nucleation limited reaction: a paucity of intermediate assembly states, a critical concentration, and kinetics displaying a lag phase. Partially formed shell intermediates were directly visualized during the growth phase by electron microscopy of the reaction mixture. The morphology of these intermediates suggests that assembly is a highly directed process. The initial rate of this reaction depends on the fifth power of the coat subunit concentration and the second or third power of the scaffolding concentration, suggesting that pentamer of coat protein and dimers or trimers of scaffolding protein, respectively, participate in the rate-limiting step.

Bacteriophage P22↗

Collectins and ficolins: sugar pattern recognition molecules of the mammalian innate immune system.

Collectins and ficolins represent two important groups of pattern recognition molecules, which bind to oligosaccharide structures on the surface of microorganisms, leading to the killing of bound microbes through complement activation and phagocytosis. Collectins and ficolins bear no significant sequence homology except for the presence of collagen-like sequences over the N-terminal halves of the polypeptides that enable the assembly of these molecules into oligomeric structures. Collectins and ficolins both contain lectin activities within the C-terminal halves of their polypeptides, the C-type carbohydrate recognition domain (CRDs) and fibrinogen beta/gamma (homology) (FBG) domain, respectively. These domains form trimeric clusters at the ends of the collagen triple helices emanating from a central hub, where the N-terminal ends of the polypeptides merge. The collectins and ficolins seem to have evolved to recognize the surface sugar codes of microbes and their binding, to these arrays of cell surface carbohydrate molecules, targets the microbe for subsequent clearance by phagocytic cells.

Animals↗

Cyanide-bridged single-molecule magnet constructed by an octacoordinated [W(CN)6(bpy)]- anion.

Two cyanide-bridged WV-M [M = Mn(II) (1), Co(II) (2)] bimetallic clusters were prepared by self-assembling a new molecular precursor [W(CN)6(bpy)]- and the corresponding metal complexes. Compound 1 shows a tetranuclear W2Mn2 entity, consisting of a Jahn-Teller ion, Mn(III), which serves as an anisotropic source, while compound 2 exhibits a trimeric W2Co structure. Among them, compound 1 displays slow relaxation of the magnetization, which is typical of a single-molecule magnet behavior.

Journal Article↗

The structure and proteolytic processing of Cbln1 complexes.

The hexadecapeptide cerebellin is present in the brains of many vertebrate species and is derived from a larger protein, Cbln1 (cerebellin 1 precursor protein). Although cerebellin has features of a neuropeptide, Cbln1 belongs to the C1q/tumor necrosis factor superfamily of secreted proteins, suggesting that it is the biologically active molecule and the proteolytic events that generate cerebellin serve another function. Therefore, we assessed whether Cbln1 undergoes proteolytic processing and determined what consequences the cleavage events necessary to produce cerebellin have on the structure of Cbln1. Substantial degradation of Cbln1 was evident in the synaptic compartment of cerebellum and lysates of cultured cerebellar neurons and cells transfected with Cbln1 expression vectors. However, only uncleaved Cbln1 containing the cerebellin motif was released and assembled into hexameric complexes. Using yeast two hybrid and mammalian expression systems we show that the cleavages required to produce cerebellin influence the subunit stoichiometry of Cbln1 complexes. Cleavage at the N-terminus of the cerebellin sequence in Cbln1 yields trimeric complexes by separating the trimer-mediating C-terminal C1q domain from conserved N-terminal cysteine residues that mediate higher order oligomerization. Cleavage at the C-terminus of the cerebellin motif disrupts the C1q domain and abolishes subunit interactions. Functional implications of these data are discussed.

Amino Acid Sequence↗

Synthesis and assembly of the synaptic cleft protein S-laminin by cultured cells.

S-laminin, a homologue of the B1 chain of laminin, is concentrated in a subset of basal laminae (BLs), including the BL at the skeletal neuromuscular junction and bears an adhesive site for motoneuron-like cells. Here, we have begun to characterize the native form of the protein. We show that several muscle- and glia-like cell lines synthesize and secrete S-laminin as well as the A, B1, and B2 subunits of the conventional laminin trimer. Experiments using subunit-specific antibodies showed that S-laminin is complexed with the A and B2 subunits of laminin but not with B1, suggesting that S-laminin replaces B1 to form a novel laminin-like trimer. Comparison of material precipitated by different antibodies provided evidence for two immunochemically distinct forms of S-laminin, both of which associate with B2 and A-like subunits. Analysis of tunicamycin-treated cells indicated that N-linked glycosylation is required neither for the selective association of S-laminin with B2 and A subunits nor for the distinction between two forms of S-laminin. Finally, a full-length S-laminin cDNA was constructed and transfected into muscle and non-muscle cells. S-laminin was detected intracellularly in both cell types, in extracellular matrix of muscle cells, and in two immunochemically distinct forms. Thus, the cDNA contains sufficient information to permit assembly, secretion, and post-translational modification of S-laminin.

Animals↗