Dense encoding

The sequence space of proteins is extremely dense. The number of possible protein sequences is 20. It is clear that even by the fastest combinatorial procedure only a very small fraction of such sequences could have been synthesized. Of course, not all of these sequences will encode protein stmctures which for functional purjDoses are constrained to have certain characteristics. A natural question that arises is how do viable protein stmctures emerge from the vast sea of sequence space The two physical features of folded stmctures are (l)in general native proteins are compact but not maximally so. (2) The dense interior of proteins is largely made up of hydrophobic residues and the hydrophilic residues are better accommodated on the surface. These characteristics give the folded stmctures a lower free energy in comparison to all other confonnations. 

The superstructure of smooth muscle actin filaments is differentiated from those of striated muscle by the absence of the troponins and the lateral organization by association of the filaments with dense bodies instead of with the Z-line. How these differences are encoded is again not at all clear. However, the myofibrillar structure and the alignment of the alternating actin and myosin filaments is apparently due primarily to dense bodies and the actin-actinin macrostructures. As the bent dumbbell shaped actins assemble into filaments they are all oriented in the same direction. The S-1 fragments of myosin will bind to actin filaments in vitro and in... 

This complex consists of at least 25 separate polypeptides, seven of which are encoded by mtDNA. Its catalytic action is to transfer electrons from NADH to ubiquinone, thus replenishing NAD concentrations. Complex I deficiency has been described in myopathic syndromes, characterized by exercise intolerance and lactic acidemia. In at least some patients it has been demonstrated that the defect is tissue specific and a defect in nuclear DNA is assumed. Muscle biopsy findings in these patients are typical of those in many respiratory chain abnormalities. Instead of the even distribution of mitochondria seen in normal muscle fibers, mitochondria are seen in dense clusters, especially at the fiber periphery, giving rise to the ragged-red fiber (Figure 10). This appearance is a hallmark of many mitochondrial myopathies. 

There is clear evidence for the involvement of three sporozoite-expressed proteins in the invasion of the salivary glands CSP, TRAP, MAEBL and four members of the LAP (LCCL/lectin adhesive-like protein family) (Raine et al., 2007) involved in sporozoite development. CSP, encoded by a single copy gene, is not found in any other apicomplexan and has been the target of many vaccine studies. CSP, is the major surface protein of the sporozoite, forming a dense coat on the parasite surface. It is presumably secreted by the apical organelles, has a signal peptide, a central domain with many amino acid repeats and a C-terminal... 

As in externally induced deformation, we should distinguish between strain-controlled and stress-controlled molecular systems. For example, deformation induced by a well-defined conformational transition (Fig. lb, bottom) can be considered as strain-controlled, where the strain is encoded by the new molecular configuration. In contrast, extension of the backbone in molecular bottlebrushes (Fig. Ic, middle) occurs at a constant tensile force controlled by steric repulsion of the densely grafted side chains. In addition to the strain distribution, it is important... 

Fig. 3 Electron micrographs of two examples of the same Pol II gene on microinjected plasmid vectors. The gene encodes Xenopus TFIII A. Note that the degree of transcript dispersal is significantly greater on the gene in panel A. The transcripts in panel B are shorter and thicker—they are less decon-densed from their native state. Common reasons for this less well-dispersed state are the presence of too much salt in the spreading drop or a pH that is less alkaline than desired (see text). Both of these genes have a discrete initiation site where the transcripts start out short (marked with a star in both panels) and a discrete termination site, beyond which transcripts are not seen (marked with a double arrowhead). The dense polymerase backbones, which can be traced from the initiation sites to the termination sites, extend approximately three-fourths of the circumference of the plasmid. The remaining one-fourth of the plasmids is not transcribed. The arrows in panel A point to RNP particles that we have been able to identify as spliceosomal particles that occur at 5 and 3 splice sites. The arrowhead in both panels points to a specific intron loop. This is the 1300-nucleotide RNA loop encoding the second intron from the 5 end of the RNA. (A) Scale bar, 0.5 /urn (B) scale bar, 0.2 /urn.

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