Real-time Bose-Einstein condensation in a finite volume with a discrete spectrum.

We show that Bose condensation in real time occurs in a finite system not only as an accumulation of the bosons in the ground state below a critical temperature, but also as a rapid enhancement of an arbitrary small symmetry breaking, followed by a very slow decay of the symmetry breaking order parameter from the almost ideal value to the vanishing equilibrium value. We show this analytically on an exactly soluble model and numerically on a model of noninteracting bosons in an oscillator potential.

NMR structure of the LCCL domain and implications for DFNA9 deafness disorder.

The LCCL domain is a recently discovered, conserved protein module named after its presence in Limulus factor C, cochlear protein Coch-5b2 and late gestation lung protein Lgl1. The LCCL domain plays a key role in the autosomal dominant human deafness disorder DFNA9. Here we report the nuclear magnetic resonance (NMR) structure of the LCCL domain from human Coch-5b2, where dominant mutations leading to DFNA9 deafness disorder have been identified. The fold is novel. Four of the five known DFNA9 mutations are shown to involve at least partially solvent-exposed residues. Except for the Trp91Arg mutant, expression of these four LCCL mutants resulted in misfolded proteins. These results suggest that Trp91 participates in the interaction with a binding partner. The unexpected sensitivity of the fold with respect to mutations of solvent-accessible residues might be attributed to interference with the folding pathway of this disulfide-containing domain.

Origin of fibronectin type II (FN2) modules: structural analyses of distantly-related members of the kringle family idey the kringle domain of neurotrypsin as a potential link between FN2 domains and kringles.

Analysis of complete genome sequences has made it clear that fibronectin type II (FN2) modules are present only in the vertebrate lineage, raising intriguing questions about the origin of this module type. Kringle domains display many similarities to FN2 domains; therefore it was suggested previously that they are highly divergent descendants of the same ancestral protein-fold. Since kringles are present in arthropodes, nematodes, and invertebrate chordates as well as in vertebrates, it is suggested that the FN2 domain arose in the vertebrate lineage through major structural modification of the more ancestral kringle fold. To explore this structural transition, in the present work we compare key structural features of two highly divergent kringle domains (the kringle of Caenorhabditis elegans Ror receptor tyrosine kinase and the kringle of rat neurotrypsin) with those of plasminogen kringles and FN2 domains. Our NMR conformation fingerprinting analysis indicates that characteristic (1)H-NMR markers of kringle or FN2 native folding, such as the dispersion of Trp aromatic connectivities and shifts of the Leu(46)/Thr(16) methyl signals, both decrease in the order kringles > neurotrypsin kringle > FN2 domains. These results suggest that the neurotrypsin kringle may represent an intermediate form between typical kringles and FN2 domains.

Subthreshold carrier-LO phonon dynamics in semiconductors with intermediate polaron coupling: a purely quantum kinetic relaxation channel.

Femtosecond transmission spectra of highly polar CdTe are compared to more covalent GaAs contrasting semiclassical kinetics with two-time quantum kinetics based on the Dyson equation. Nonequilibrium heavy holes in CdTe show ultrafast energy redistribution via the Fröhlich mechanism even if photoexcited below the LO phonon energy. This subthreshold relaxation is a genuine quantum kinetic effect. It gains importance if the polaron self-energy is comparable to the phonon energy. Conservation of the free-particle energies is not required under these conditions.

Bose-Einstein condensation quantum kinetics for a gas of interacting excitons.

A quantum kinetics of the Bose-Einstein condensation in the self-consistent (s.c.) Hartree-Fock-Bogoliubov (HFB) model of the interacting Bose gas is formulated and numerically solved for the example of excitons scattering with a thermal bath of acoustic phonons. The theory describes the condensation in real time starting from a nonequilibrium initial state towards the equilibrium HFB solution. The s.c. changes of the spectrum are automatically incorporated in the scattering terms.

Gelatin-binding region of human matrix metalloproteinase-2: solution structure, dynamics, and function of the COL-23 two-domain construct.

Human matrix metalloproteinase-2 (MMP-2) contains an array of three fibronectin type II (FII) modules postulated to interact with gelatin (denatured collagen). Here, we verify that the NMR solution structure of the third FII repeat (COL-3) is similar to that of the second FII repeat (COL-2); characterize its ligand-binding properties; and derive dynamics properties and relative orientation in solution for the two domains of the COL-23 fragment, a construct comprising COL-2 and COL-3 in tandem, with each domain possessing a putative collagen-binding site. Interaction of the synthetic gelatin-like octadecapeptide (Pro-Pro-Gly)(6) (PPG6) with COL-3 is weaker than with COL-2. We found that a synthetic peptide comprising segment 33-42 (peptide 33-42) from the MMP-2 prodomain interacts with COL-3 and, albeit with lower affinity, with COL-2 in a way that mimics PPG6 binding. COL-3 strongly prefers peptide 33-42 over PPG6, which suggests that intramolecular interactions with the prodomain could modulate binding of pro-MMP-2 to its gelatin substrate. In COL-23, the two modules retain their structural individuality and tumble independently. Overall, the NMR data indicate that the relative orientation of the modules in COL-23 is not fixed in solution, that the modules do not interact with one another, and that COL-23 is rather flexible. The binding sites face opposite each other, and their responses to, and normalized affinities for, the longer ligand PPG12 are virtually identical to those of the individual domains for PPG6, thus precluding co- operativity, although they may interact simultaneously with multiple sites of the extracellular matrix.

A human protein containing multiple types of protease-inhibitory modules.

By using sensitive homology-search and gene-finding programs, we have found that a genomic region from the tip of the short arm of human chromosome 16 (16p13.3) encodes a putative secreted protein consisting of a domain related to the whey acidic protein (WAP) domain, a domain homologous with follistatin modules of the Kazal-domain family (FS module), an immunoglobulin-related domain (Ig domain), two tandem domains related to Kunitz-type protease inhibitor modules (KU domains), and a domain belonging to the recently defined NTR-module family (NTR domain). The gene encoding these WAP, FS, Ig, KU, and NTR modules (hereafter referred to as the WFIKKN gene) is intron-depleted--its single 1,157-bp intron splits the WAP module. The validity of our gene prediction was confirmed by sequencing a WFIKKN cDNA cloned from a lung cDNA library. Studies on the tissue-expression pattern of the WFIKKN gene have shown that the gene is expressed primarily in pancreas, kidney, liver, placenta, and lung. As to the function of the WFIKKN protein, it is noteworthy that it contains FS, WAP, and KU modules, i.e., three different module types homologous with domains frequently involved in inhibition of serine proteases. The protein also contains an NTR module, a domain type implicated in inhibition of zinc metalloproteinases of the metzincin family. On the basis of its intriguing homologies, we suggest that the WFIKKN protein is a multivalent protease inhibitor that may control the action of multiple types of serine proteases as well as metalloproteinase(s).

The LCCL module.

Here we show that Lgl1 protein, cub-1-related proteins, coch-5b2-related proteins, coagulation factor C of horse-shoe crab and a predicted protein of Plasmodium falciparum share a homologous domain. Since this domain-type was first identified in Limulus factor C, Coch-5b2 and Lgl1 we propose the name LCCL for this domain-family. The LCCL module of coch-5b2 is of special biological interest because it has been shown recently that mutations affecting this module cause the deafness disorder DFNA9 in humans. With a view to defining the structure and function of the LCCL domain of human coch-5b2 protein, we have expressed it in Escherichia coli and subjected it to preliminary structural characterization. Structure prediction and circular dichroism studies on the recombinant protein indicate that the domain possesses both alpha helices and beta strands. It is shown that the mutations which cause hearing loss in humans affect residues that are critical for the integrity of the LCCL module of the coch-5b2 protein.

The PAN module: the N-terminal domains of plasminogen and hepatocyte growth factor are homologous with the apple domains of the prekallikrein family and with a novel domain found in numerous nematode proteins.

Based on homology search and structure prediction methods we show that (1) the N-terminal N domains of members of the plasminogen/hepatocyte growth factor family, (2) the apple domains of the plasma prekallikrein/coagulation factor XI family, and (3) domains of various nematode proteins belong to the same module superfamily, hereafter referred to as the PAN module. The patterns of conserved residues correspond to secondary structural elements of the known three-dimensional structure of hepatocyte growth factor N domain, therefore we predict a similar fold for all members of this superfamily. Based on available functional informations on apple domains and N domains, it is clear that PAN modules have significant functional versatility, they fulfill diverse biological functions by mediating protein-protein or protein-carbohydrate interactions.

The second type II module from human matrix metalloproteinase 2: structure, function and dynamics.

BACKGROUND: Matrix metalloproteinase 2 (MMP-2, gelatinase A, 72 kDa type IV collagenase) has an important role in extracellular matrix degradation during cell migration and tissue remodeling. It is involved in development, inflammation, wound healing, tumor invasion, metastasis and other physiological and pathological processes. The enzyme cleaves several types of collagen, elastin, fibronectin and laminin. Binding to collagen is mediated by three repeats homologous to fibronectin type II modules, which are inserted in the catalytic domain in proximity to the active site. RESULTS: We have determined the NMR solution structure of the second type II module from human MMP-2 (col-2). The module exhibits a typical type II fold with two short double-stranded antiparallel beta sheets and three large loops packed around a cluster of conserved aromatic residues. Backbone amide dynamics, derived from (15)N relaxation experiments, correlate well with solvent accessibility and intramolecular hydrogen bonding. A synthetic peptide with the collagen consensus sequence, (Pro-Pro-Gly)(6), is shown to interact with the module. CONCLUSIONS: Spectral perturbations induced by (Pro-Pro-Gly)(6) binding reveal the region involved in the interaction of col-2 with collagen. The binding surface comprises exposed aromatic residues Phe21, Tyr38, Trp40, Tyr47, Tyr53 and Phe55, and the neighboring Gly33-Gly37 segment.

The NTR module: domains of netrins, secreted frizzled related proteins, and type I procollagen C-proteinase enhancer protein are homologous with tissue inhibitors of metalloproteases.

Using homology search, structure prediction, and structural characterization methods we show that the C-terminal domains of (1) netrins, (2) complement proteins C3, C4, C5, (3) secreted frizzled-related proteins, and (4) type I procollagen C-proteinase enhancer proteins (PCOLCEs) are homologous with the N-terminal domains of (5) tissue inhibitors of metalloproteinases (TIMPs). The proteins harboring this netrin module (NTR module) fulfill diverse biological roles ranging from axon guidance, regulation of Wnt signaling, to the control of the activity of metalloproteases. With the exception of TIMPs, it is not known at present what role the NTR modules play in these processes. In view of the fact that the NTR modules of TIMPs are involved in the inhibition of matrixin-type metalloproteases and that the NTR module of PCOLCEs is involved in the control of the activity of the astacin-type metalloprotease BMP1, it seems possible that interaction with metzincins could be a shared property of NTR modules and could be critical for the biological roles of the host proteins.

Amoebapore homologs of Caenorhabditis elegans.

It is shown that the Caenorhabditis elegans genome contains several distantly related members of the gene family of saposin-like proteins. The putative products of genes T07C4.4, T08A9.7A, T08A9.7B, T08A9.8, T08A9.9, T08A9.10 are similar to the amoebapores of Entamoeba histolytica, granulysin of cytotoxic T lymphocytes and a putative amoebapore-related protein of the liver fluke Fasciola hepatica inasmuch as they consist of only a single saposin-like domain and a secretory signal peptide. The saposin-like domain of protein T07C4.4, which is most closely related to NK-lysin and granulysin, has been expressed in Escherichia coli and the recombinant protein was shown to have a circular dichroism spectrum consistent with the helix bundle structure characteristic of saposin-like domains. Recombinant T07C4.4 protein was found to have antibacterial activity, suggesting that these amoebapore homologs may play a role in antibacterial mechanisms of C. elegans.

Structure and domain-domain interactions of the gelatin binding site of human 72-kilodalton type IV collagenase (gelatinase A, matrix metalloproteinase 2).

We have shown previously that all three fibronectin type II modules of gelatinase A contribute to its gelatin affinity. In the present investigation we have studied the structure and module-module interactions of this gelatin-binding domain by circular dichroism spectroscopy and differential scanning calorimetry. Comparison of the Tm values of the thermal transitions of isolated type II modules with those of bimodular or trimodular proteins has shown that the second type II module is significantly more stable in the trimodular protein coll 123 (Tm = 54 degrees C) than in the single-module protein coll 2 (Tm = 44 degrees C) or in the bimodular proteins coll 23 (Tm = 47 degrees C) and coll 12 (Tm = 48 degrees C). Analysis of the enthalpy changes associated with thermal unfolding of the second type II module suggests that it is stabilized by domain-domain interactions in coll 123. We propose that intimate contacts exist between the three tandem type 11 units and they form a single gelatin-binding site. Based on the three-dimensional structures of homologous metalloproteases and type II modules, a model is proposed in which the three type II units form an extension of the substrate binding cleft of gelatinase A.

The gelatin-binding site of human 72 kDa type IV collagenase (gelatinase A).

To identify structures critical for gelatin-binding of 72 kDa type IV collagenase (gelatinase A), fragments of this metalloproteinase have been expressed in Escherichia coli and assayed for their gelatin affinity. Each of the three fibronectin-related type II domains was found to have affinity for gelatin. Fragments containing all three tandem type II domains had significantly stronger affinity than any of the constituent units, indicating that they co-operate to form the high-affinity gelatin-binding site. Competition experiments have also shown that gelatinase A binds more tightly to gelatin than fibronectin and can displace the latter from denatured collagen.