A new journal – "Theoretical Biology and Medical Modelling"

Biology has a conceptual basis that allows one to build models and theorize across many life sciences, including medicine and medically-related disciplines. A dearth of good venues for publication has been perceived during a period when bioinformatics, systems analysis and biomathematics are burgeoning.     

A polypeptide "building block" for the β-trefoil fold identified by "top-down symmetric deconstruction"

Fibroblast growth factor-1, a member of the 3-fold symmetric β-trefoil fold, was subjected to a series of symmetric constraint mutations in a process termed “top-down symmetric deconstruction.” The mutations enforced a cumulative exact 3-fold symmetry upon symmetrically equivalent positions within the protein and were combined with a stability screen. This process culminated in a β-trefoil protein with exact 3-fold primary-structure symmetry that exhibited excellent folding and stability properties. Subsequent fragmentation of the repeating primary-structure motif yielded a 42-residue polypeptide capable of spontaneous assembly as a homotrimer, producing a thermostable β-trefoil architecture. The results show that despite pronounced reduction in sequence complexity, pure symmetry in the design of a foldable, thermostable β-trefoil fold is possible. The top-down symmetric deconstruction approach provides a novel alternative means to successfully identify a useful polypeptide “building block” for subsequent “bottom-up” de novo design of target protein architecture.     

Good Enough for Government Work? A Study in "Grey Archeology"

Archaeological Salvage Excavations at Patoka Lake, Indiana: Prehistoric Occupations of the Upper Patoka River Valley . Cheryl Ann Munson , ed. Glen A. Black Laboratory of Archaeology Research Reports, No. 6. Bloomington: Indiana University, 1980. xxvii + 829 pp. $15.00 (paper).
Colonization and Conquest: The 1980 Archaeological Excavations at Fort Toulouse and Fort Jackson, Alabama . Gregory A. Waselkov, Brian M. Wood , and Joseph M. Herbert . Auburn University Archaeological Monograph No. 4. Montgomery, AL: Auburn University, 1982. xxix + 399 pp. $11.00 (paper).
The Kellogg Village Site Investigations: Clay County, Mississippi . James R. Atkinson, John C. Phillips , and Richard Walling . A Report of work undertaken in cooperation with the U.S. Army Corps of Engineers, Mobile District, in fulfillment of Modification Three to Contract DACW 01–77–0015. Starkville: Mississippi State University, 1980. x + 345 pp. n.p. (paper).
Parkin: The 1978–1979 Archaeological Investigations of a Cross County, Arkansas Site . Phyllis A. Morse . Arkansas Archaeological Survey Research Series, No. 13. Fay-etteville: University of Arkansas, 1981. 110 pp. $6.00 (paper).
The Shallow Lake Site (3Un9/52) and Its Place in Regional Prehistory . Martha A. Rolingson and Frank F. Schambach . Arkansas Archaeological Survey Research Series, No. 12. Fayetteville: University of Arkansas, 1981. 240 pp. $10.00 (paper).
Yellow Creek Archaeological Project: Volume 1 . Robert M. Thome, Bettye J. Broyles , and Jay K. Johnson . Archaeological Papers of the Center for Archaeological Research, No. 1. Chattanooga: Tennessee Valley Authority, 1981. 354 pp. $13.00 (paper).
Yellow Creek Archaeological Project: Volume 2 . Jay K. Johnson . Archaeological Papers of the Center for Archaeological Research, No. 2. Chattanooga: Tennessee Valley Authority, 1981. 347 pp. $13.00 (paper).     

"Janus" Cyclic Peptides: A New Approach to Amyloid Fibril Inhibition?

Cyclic peptides are increasingly being shown as powerful inhibitors of fibril formation, and have the potential to be therapeutic agents for combating many debilitating amyloid-related diseases. One such example is a cyclic peptide derivative from the human apolipoprotein C-II, which has the ability to inhibit fibril formation by the fibrillogenic peptide apoC-II(60–70). Using classical molecular dynamics and electronic structure calculations, we were able to provide insight into the interaction between the amyloidogenic peptide apoC-II(60–70) and its cyclic derivative, cyc(60–70). Our results showed that cyc(60–70) induced increased flexibility in apoC-II(60–70), suggesting that one mechanism by which cyc(60–70) inhibits fibrillisation is by destabilising apoC-II(60–70) structure, rendering it incapable of adopting fibril favouring conformations. In contrast, cyc(60–70) shows less flexibility upon binding to apoC-II(60–70), which is predominantly mediated by hydrophobic interactions between the aromatic rings of the peptides. This effectively creates a cap around the fibril-forming region of apoC-II(60–70) and generates an outer hydrophilic shell that discourages further apoC-II(60–70) peptide self-association. We showed that apoC-II(60–70) exhibited stronger binding affinity for the hydrophobic face of cyc(60–70) and weakest binding affinity for the hydrophilic side. This suggests that cyc(60–70) can be an effective fibril inhibitor due to its amphipathic character, like that of the "Janus"-type particles. This property can be exploited in the design of specific inhibitors of amyloid fibril formation.     

Who put the "A" in Atg12: autophagy or apoptosis?

Much deliberation surrounds how the two homeostatic pathways, autophagy and apoptosis, converge; in the December 9 issue of Molecular Cell, Rubinstein et al. (2011) identify a proapoptotic role for the autophagic protein Atg12, based on a BH3-like domain, which enables binding and inhibition of antiapoptotic Bcl-2 family proteins.     

A "two-hit" model of cystogenesis in autosomal dominant polycystic kidney disease?

An intriguing feature of autosomal dominant polycystic kidney disease (ADPKD) is the focal and sporadic nature of individual cyst formation. Typically, only a few renal cysts are detectable in an affected individual during the first two decades of life. By the fifth decade, however, hundreds to thousands of renal cysts can be found in most patients. Additionally, significant intra-familial variability of ADPKD has been well documented. Taken together, these findings suggest that factor(s) in addition to the germline mutation of a polycystic kidney disease gene might be required for individual cyst formation. Indeed, recent studies have provided compelling evidence in support of a "two-hit" model of cystogenesis in ADPKD. In this model, inactivation of both copies of a polycystic kidney disease gene by germline and somatic mutations within an epithelial cell provides growth advantages for it to proliferate clonally into a cyst. This article highlights key findings of these recent studies and discusses the controversies and implications of the "two-hit" model in ADPKD.     

A role for voltage gated T-type calcium channels in mediating "capacitative" calcium entry?

Calcium entry through plasma membrane calcium channels is one of the most important cell signaling mechanism involved in such diverse functions as secretion, contraction and cell growth by regulating gene expression, proliferation and apoptosis. The identity of plasma membrane calcium channels, the main regulators of calcium entry, involved in cell proliferation has been thus extensively sought. Among these, a calcium entry pathway called capacitative calcium entry (CCE), activated by calcium store depletion, is particularly important in non-excitable cells. Though this capacitative calcium entry is generally supposed to occur through TRP channels there is some evidence that voltage-dependent T-type calcium channels may contribute to calcium entry after store depletion. Here we show that though mibefradil, a T-type calcium channel blocker, is able to reduce capacitative calcium entry induced by either thapsigargin or ATP, this was not mimicked by any other T-type calcium channel inhibitors even in cells overexpressing alpha(1H) T-type calcium channels, leading us to conclude that T-type calcium channels are not responsible for the capacitative calcium entry observed in different cancer cell lines. On the contrary, we show that the action of mibefradil on capacitative calcium entry is due to an action on store-operated calcium channels.     

Do chondrocytes undergo "activation" and "transdifferentiation" during the pathogenesis of osteoarthritis? A review of the ultrastructural and immunohistochemical evidence

Chondrocytes, which are the only cell type in the articular cartilage, show substantial morphological and functional differences, depending on their location within the tissue. In OA cartilage, outstanding modifications have been reported concerning their structure and functions. Based on the principle that both structure and function run in a parallel manner, new concepts are arising related to morphological observations. Observations on OA chondrocytes, such as cytoskeleton disruption, development of the secretory machinery (rough endoplasmic reticulum and Golgi complex), and cell death by apoptosis, among others, certainly must be related to the role of chondrocytes in OA pathogenesis. In this degradative process, it has been acknowledged that cell death, matrix degradation and subchondral bone remodelling are the main causes of cartilage breakdown in osteoarthritis. The aim of this review was to correlate and integrate in a logical manner the modifications of chondrocytes with cartilage breakdown during osteoarthritis pathogenesis. Furthermore, we intend to open a debate on cell cycle and mitosis, as well as on signalling molecules that might be involved in the morphofunctional changes in OA chondrocytes, which we propose to name "activation" and "transdifferentiation" of chondrocytes. We expect this analysis to be useful for studying OA pathogenesis in depth, with the aim of finding new strategies for the early diagnosis and therapeutic procedures for this invalidating disease, which is already an important public health problem.     

A "Neural" Enzyme in Nonbilaterian Animals and Algae: Preneural Origins for Peptidylglycine α-Amidating Monooxygenase

Secreted peptides, produced by enzymatic processing of larger precursor molecules, are found throughout the animal kingdom and play important regulatory roles as neurotransmitters and hormones. Many require a carboxy-terminal modification, involving the conversion of a glycine residue into an α-amide, for their biological activity. Two sequential enzymatic activities catalyze this conversion: a monooxygenase (peptidylglycine α-hydroxylating monooxygenase or PHM) and an amidating lyase (peptidyl-α-hydroxyglycine α-amidating lyase or PAL). In vertebrates, these activities reside in a single polypeptide known as peptidylglycine α-amidating monooxygenase (PAM), which has been extensively studied in the context of neuropeptide modification. Bifunctional PAMs have been reported from some invertebrates, but the phylogenetic distribution of PAMs and their evolutionary relationship to PALs and PHMs is unclear. Here, we report sequence and expression data for two PAMs from the coral Acropora millepora (Anthozoa, Cnidaria), as well as providing a comprehensive survey of the available sequence data from other organisms. These analyses indicate that bifunctional PAMs predate the origins of the nervous and endocrine systems, consistent with the idea that within the Metazoa their ancestral function may have been to amidate epitheliopeptides. More surprisingly, the phylogenomic survey also revealed the presence of PAMs in green algae (but not in higher plants or fungi), implying that the bifunctional enzyme either predates the plant/animal divergence and has subsequently been lost in a number of lineages or perhaps that convergent evolution or lateral gene transfer has occurred. This finding is consistent with recent discoveries that other molecules once thought of as "neural" predate nervous systems.     

A simple "proximity" correction for Förster resonance energy transfer efficiency determination in membranes using lifetime measurements

Accurate measurements of oligomerization in membranes by Förster resonance energy transfer (FRET) are always compromised by a substantial contribution from random chance colocalization of donors and acceptors. Recently, Li and coworkers demonstrated the use of computer simulation in estimating the contribution of this “proximity” component to correct the FRET efficiency and estimate the free energy of dimer formation of the G380R mutants of fibroblast growth factor receptor 3 (FGFR3) transmembrane domain immersed into lipid bilayer. Because tight dimerization will result in complete energy transfer from donor to acceptor, we have used the same experimental system of fluorescein- and rhodamine-labeled G380R mutants of FGFR3 for the experimental assessment of the proximity FRET corrections using fluorescence lifetime measurements. The experimental proximity FRET correction, based on time-resolved fluorescence measurements, is expected to have general advantages over theoretical correction, especially in the case of nonrandomly distributed monomers.     

Is the HemK family of putative S-adenosylmethionine-dependent methyltransferases a "missing" zeta subfamily of adenine methyltransferases? A hypothesis

Previous comparative studies revealed close similarity among various groups of S-adenosyl-L-methionine (AdoMet)-dependent methyltransferases (MTases), indicating their common evolutionary origin. We present evidence for a remarkable similarity between the sequence and predicted structure of HemK (a widespread family of putative proteins encoded in genomes from bacteria to humans) and the catalytic domain of the gamma-subfamily of adenine-specific DNA MTases (N6mA MTases). We predict the structure and function of the putative catalytic domain of HemK proteins and speculate that the target-recognizing function may be conferred by the N-terminal variable region.