Chromatin replication: Finding the right connection.

Nucleosomes are preferentially assembled on replicating DNA by chromatin assembly factor 1; recent studies have shown that replicated DNA is marked for assembly into chromatin by the replication-fork-associated protein PCNA.     

Finding the right organelle. Targeting signals in mitochondrial outer-membrane proteins

The mitochondrial outer membrane contains a diverse set of proteins that includes enzymes, components of the preprotein translocation machinery, pore-forming proteins, regulators of programmed cell death, and those that control the morphology of the organelle. All these proteins, like the vast majority of mitochondrial proteins, are encoded in the nucleus, so they are synthesized in the cytosol and contain signals that are essential for their subsequent import into mitochondria. This review summarizes our current knowledge of the signals that target mitochondrial outer-membrane proteins to their correct intracellular location. In addition, the mechanisms by which these signals are decoded by the mitochondria are discussed.     

Finding the fittest fold: using the evolutionary record to design new proteins

For many years, the holy grail of protein engineering has been the design of artificial amino acid sequences that fold into stable proteins with desired functions. In the current issue of Nature, two papers from the Ranganathan group (Russ et al., 2005; Socolich et al., 2005) report remarkable success in the design of artificial WW domains. Their method, termed statistical coupling analysis (Lockless and Ranganathan, 1999), does not use structural or physicochemical information but instead extracts information about essential patterns of amino acids from the evolutionary record.     

Finding the right RNA: identification of cellular mRNA substrates for RNA-binding proteins.

Defects in RNA-binding proteins have been implicated in human genetic disorders. However, efforts in understanding the functions of these proteins have been hampered by the inability to obtain their mRNA substrates. To identify cognate cellular mRNAs associated with an RNA-binding protein, we devised a strategy termed isolation of specific nucleic acids associated with proteins (SNAAP). The SNAAP technique allows isolation and subsequent identification of these mRNAs. To assess the validity of this approach, we utilized cellular mRNA and protein from K562 cells and alphaCP1, a protein implicated in a-globin mRNA stability, as a model system. Immobilization of an RNA-binding protein with the glutathione-S-transferase (GST) domain enables isolation of mRNA within an mRNP context and the identity of the bound mRNAs is determined by the differential display assay. The specificity of protein-RNA interactions was considerably enhanced when the interactions were carried out in the presence of cellular extract rather than purified components. Two of the mRNAs specifically bound by alphaCP1 were mRNAs encoding the transmembrane receptor protein, TAPA-1, and the mitochondrial cytochrome c oxidase subunit II enzyme, coxII. A specific poly(C)-sensitive complex formed on the TAPA-1 and coxII 3' UTRs consistent with the binding of aCP1. Furthermore, direct binding of purified alphaCP proteins to these 3' UTRs was demonstrated and the binding sites determined. These results support the feasibility of the SNAAP technique and suggest a broad applicability for the approach in identifying mRNA targets for clinically relevant RNA-binding proteins that will provide insights into their possible functions.     

Rhytidectomy and the nasolabial fold.

I describe a technical modification in the Skoog face lift procedure that releases the deep attachments of the SMAS to the muscles of facial expression for maximal mobility of the medial cheek yet elevates the cheek flap as a composite of skin, subcutaneous tissue, and SMAS to enhance skin perfusion. My results with the procedure in 100 patients are analyzed by using functional zones of the nasolabial fold corresponding to underlying musculature and a simple grading system based on preoperative and postoperative photographs. Marked improvement in the nasolabial fold was noted in over 80 percent of patients by 6 and 12 months postoperatively. This effect seemed to last up to 4 years.     

Motif-based fold assignment.

Conventional fold recognition techniques rely mainly on the analysis of the entire sequence of a protein. We present an MBA method to improve performance of any conventional sequence-based fold assignment. The method uses sequence motifs, such as those defined in the Prosite database, and the SwissProt annotation of the fold library. When combined with a simple SDP method, the coverage of MBA is comparable to the results obtained with PSI-BLAST. However, the set of the MBA predictions is significantly different from that of PSI-BLAST, leading to a 40% increase of the coverage for the combined MBA/PSI-BLAST method. The MBA approach can be easily adopted to include the results of sequence-independent function prediction methods and alternative motif and annotation databases. The method is available through the web server localized at http://www.doe-mbi.ucla.edu/mba.     

The SMAS and the nasolabial fold.

In a series of histologic sections and clinical and cadaver dissections, the superficial musculoaponeurotic system (SMAS) is seen to become the investing fascia of the zygomaticus major and minor muscles in the medial cheek. The pull on the cheek flap during rhytidectomy is diffused by the attachment of the SMAS to these muscles. I believe that this attachment accounts for the minimal change in the nasolabial crease after a Skoog-type sub-SMAS face lift.     

Neuropoietic cytokines in the hematopoietic fold.

Among the molecules that determine the developmental fate of sympathetic neurons from noradrenergic to cholinergic function are two apparently unrelated proteins, cholinergic differentiation factor and ciliary neurotrophic factor (CDF and CNTF, respectively). The present work suggests a structural basis for their functional overlap: sequence pattern-matching and predictive structure analysis contends that CDF and CNTF are homologous and share a common helical framework. An integrated CDF/CNTF profile also reveals similar sequence/structure motifs in a group of hematopoietic cytokines composed of granulocyte colony-stimulating factor, interleukin-6, and a novel factor called oncostatin M; a more distant relationship is indicated with interleukin-3 and interferons-alpha/beta. Evolutionary ties between neuropoietic and hematopoietic cytokines predict a distinctive tertiary architecture for the uncharacterized CDF and CNTF receptors. The intertwined cytokine/receptor networks signal a closer relationship between the molecular mechanisms underlying neuro- and hematopoiesis.     

Anatomic variations of the nasolabial fold.

The nasolabial fold varies considerably from person to person. Three main groups may be distinguished: convex, concave, and straight. It is the muscles of smiling that are directly responsible for the shape and depth of the fold, and in their absence of function, as in facial palsy, the nasolabial fold disappears. Cadavers were selected in accordance with the nasolabial fold they presented and were dissected to analyze the difference in underlying anatomy between one fold shape in one cadaver and another fold shape in another. The study demonstrates that the nasolabial fold is the result of a conflict between soft and dynamic tissues of the middle face or an interaction between the skin and fat envelope on one side and the underlying muscles on the other. The greater this conflict, the more excess there is of cheek skin and the more pronounced a nasolabial fold. The mechanism that creates the nasolabial fold and the anatomy of the fold are described in this paper.