Mandibular and temporomandibular joint arthropathy in the differential diagnosis of the parotid mass.

OBJECTIVE: To increase awareness of temporomandibular joint and mandibular disease in the overall evaluation and diagnosis of the parotid mass. STUDY DESIGN: We describe clinical presentations of pigmented villonodular synovitis and synovial chondrocalcinosis of the temporomandibular joint, as well as osteoma of the mandible, as they may initially suggest primary neoplasms of the parotid gland. CONCLUSIONS: Preauricular swelling is a common presenting symptom for patients visiting an otolaryngologist. Often this symptom is suggestive of a parotid mass. However, lesions of the temporomandibular joint and mandible may also present in this fashion.

Conformational toxicity and sporadic conformational diseases.

Spontaneous, so-called 'conformational' diseases, specially of the neurodegenerative type like Alzheimer's, are linked to certain protein types which have the normal amino-acid sequence but are misfolded and accumulate due to resistance to proteolysis. In the case of prion diseases, the 'protein only' hypothesis assumes that the misconformation of a native protein could be initiated upon interaction with a sister-protein already in the misfolded state. There is an alternative to this sister protein contamination scheme, which assumes that the misconformation is acquired upon protein synthesis, that is de novo. Misfoldling and resistance to proteolysis could result from defects responsible for shortage or inactivity of the cellular factors in charge of protein folding and degradation. The defects could have a genetic origin (the gene of the faulty factor involved could have been mutated, or control and regulation of its expression could have been altered, etc.). Alternatively, the cell's actual biosynthetic and/or proteolytic resources could have become overloaded and unavailable, due to unscheduled mass-production of proteins resulting from unscheduled cell growth or proliferation, cell stress, etc. Xenobiotics, active for instance as endocrine proliferators, stressors, or inducing copious, unscheduled gene expression, etc. could give rise to shortage of cellular factors necessary for the production of native proteins and for proteolysis. Alternatively, xenobiotics could alter expression or activity of some of these factors. In both cases, the xenobiotic could be a 'conformational toxicant' by inducing misfolding of selected proteins. The xenobiotic could trigger some conformational disease if it targets a specific protein and tissue.

Ribosome traffic in E. coli and regulation of gene expression.

The ribosome traffic during translation of E. coli coding sequences was simulated, assuming that the rate of translation of individual codons is limited by the cognate tRNA availability. Actual translation rates were taken from Solomovici et al. (J. theor. Biol. 185, 511-521, 1997). The mean translation rates of the 4271 sequences cover a broad, two-fold range, whereas the local rate of translation along messengers varies three-fold on average. The simulation allows one to sketch the ribosome traffic on the polysome, in particular by providing the extent of mRNA sequences uncovered between consecutive ribosomes and the time during which these sequences are exposed. These parameters may participate in the control of mRNA stability and transcriptional polarity. By averaging the translation rates in a 17-codon window, assumed to be the sequence covered by a translating ribosome, and sliding this window along a given coding sequence, the addresses KMAX and KMIN, and the times TMAX and TMIN of respectively the slowest and the fastest translated window were determined. It is shown that under the assumptions made, TMAX sets the number of proteins translated from a given mRNA molecule per unit time, in case the delay between consecutive translation starts is below TMAX. Both windows display two strong biases, one as expected on the usage of codon frequencies, and the other surprisingly on the occurrence of amino acids.

Synonymous codon substitutions affect ribosome traffic and protein folding during in vitro translation.

To investigate the possible influence of the local rates of translation on protein folding, 16 consecutive rare (in Escherichia coli) codons in the chloramphenicol acetyltransferase (CAT) gene have been replaced by frequent ones. Site-directed silent mutagenesis reduced the pauses in translation of CAT in E. coli S30 extract cell-free system and led to the acceleration of the overall rate of CAT protein synthesis. At the same time, the silently mutated protein (with unaltered protein sequence) synthesized in the E. coli S30 extract system was shown to possess 20% lower specific activity. The data suggest that kinetics of protein translation can affect the in vivo protein-folding pathway, leading to increased levels of protein misfolding.

Detection of transmembrane helical segments at the nucleotide level in eukaryotic membrane protein genes.

The analysis of base distributions at the three codon positions, in sequences coding for polytopic membrane proteins from Eukaryotes, reveals a global excess of thymine and a depletion of adenine, at the second codon position. These genes were scanned using a sliding window, in which the average ratio of T over A at the second position of codons was computed. The scan shows that sharp peaks of this ratio, which are responsible for the high mean value of this parameter in the genes, correlate closely with the transmembrane segments of the membrane proteins. These results are quite similar to our previous findings for bacterial polytopic inner membrane proteins. This establishes the ratio of T over A at codon position two as a universal parameter for both the characterization of the genes of polytopic membrane proteins, and for the location of alpha-helical, transmembrane segments of these proteins.

Differential resistance to proteinase K digestion of the yeast prion-like (Ure2p) protein synthesized in vitro in wheat germ extract and rabbit reticulocyte lysate cell-free translation systems.

The Ure2p yeast prion-like protein was translated in vitro in the presence of labeled [35S]methionine in either rabbit reticulocyte lysate (RRL) or wheat germ extract (WGE) cell-free systems. When subjected to proteinase K digestion, the Ure2p protein synthesized in WGE was proteolysed much more slowly compared to that synthesized in RRL; this displays fragments of about 31-34 kDa, persisting over 8 min. Thus, the digestion rate and pattern of the protein synthesized in WGE, unlike that synthesized in RRL, revealed characteristic features of the [URE3] prion-like isoform of the Ure2p protein [Masison, D.C. and Wickner, R.B. (1995) Science 270, 93-95]. Chloramphenicol acetyltransferase, synthesized under the same conditions, differed fundamentally in its proteolytic sensitivity toward proteinase K (PK); in the RRL system it was more slowly digested than in WGE, proving specific PK inhibitors to be absent in both systems. Posttranslational addition of the WGE to the RRL-synthesized Ure2p does not protect Ure2p from efficient PK degradation either. The differences in Ure2p degradation may be ascribed to a specific structure or specific states of association of Ure2p synthesized in WGE; obviously, they yield a protein that mimics the behavior of the Ure2p in [URE3] yeast strains. The present data suggest that particular conditions of the Ure2p protein translation and/or certain cellular components (accessory proteins and extrinsic factors), as well as the nature of the translation process itself, could affect the intracellular folding pathway of Ure2p leading to the de novo formation of the prion [URE3] isoform.

Does Escherichia coli optimize the economics of the translation process?

The codon translation rate is usually assumed to be proportional to the cellular concentration of the cognate tRNA, but synonymous codons sharing the same cognate tRNA may be translated at rather different rates. To account for the latter observation, we assume that the translation process is optimized in two respects: (i), the codon demand is optimized with respect to the supply of cognate tRNAs (composition of the tRNA pool); and (ii), for synonymous codons sharing the same cognate tRNA, the usage frequency of each codon correlates optimally with the stability of the codon-anticodon complex. These assumptions allow us to compute the relative rate constants of synonymous codons. Highly expressed genes, which produce 80-90% of the protein mass in the E. coli cell, appear to have selected codons which make an optimal use of the tRNA pool. Assuming the optimization criteria were valid, a list of codon translation times (in ms) were derived from available experimental data.

A method to detect transmembrane helical segments at the nucleotide level.

The analysis of base distributions at the three codon positions, in sequences coding for integral inner membrane proteins from Bacteria, reveal a global excess of thymine and a depletion of adenine, at codon position two. These genes were scanned using a sliding window, in which the average ratio of T to A at the second position of codons, TA(2) (converted to a logarithm, the LTA2 ratio) was computed. The profiles obtained reveal sharp and local peaks of the LTA2 ratio, which account for the high mean values of this parameter. For inner membrane proteins of known structure, the position and extent of these peaks correlate with the location of transmembrane alpha-helices. The prediction accuracy of the detection of such structures using the LTA2 ratio compares to that obtained using algorithms based on an hydrophobicity index of amino-acids. This new criterion presents several advantages, as it deals directly with the nucleotide sequence, does not rely on the values of empirical parameters and finds direct applications in molecular biology studies. Since the nucleotide sequences of transmembrane beta-strands do not give rise to peaks in the LTA2 ratio profile, the criterion appears to characterize exclusively alpha-helical segments in transmembrane proteins.