Biochemical analysis of the 20 S proteasome of Trypanosoma brucei
ABSTRACT We describe here biochemical characterization of the 20 S proteasome from the parasitic protozoan Trypanosoma brucei. Similar to the mammalian proteasome, the T. brucei proteasome is made up of seven alpha- and seven beta-subunits. Of the seven beta-type subunits, five contain pro-sequences that are proteolytically removed during assembly, and three of them are predicted to be catalytic based on primary sequence. Affinity labeling studies revealed that, unlike the mammalian proteasome where three beta-subunits were labeled by the affinity reagents, only two beta-subunits of the T. brucei proteasome were labeled in the complex. These two subunits corresponded to beta2 and beta5 subunits responsible for the trypsin-like and chymotrypsin-like proteolytic activities, respectively. Screening of a library of 137,180 tetrapeptide fluorogenic substrates against the T. brucei 20 S proteasome confirmed the nominal beta1-subunit (caspase-like or PGPH) activity and identified an overall substrate preference for hydrophobic residues at the P1 to P4 positions in a substrate. This overall stringency is relaxed in the 11 S regulator (PA26)-20 S proteasome complex, which shows both appreciable activities for cleavage after acidic amino acids and a broadened activity for cleavage after basic amino acids. The 20 S proteasome from T. brucei also shows appreciable activity for cleavage after P1-Gln that is minimally observed in the human counterpart. These results demonstrate the importance of substrate sequence specificity of the T. brucei proteasome and highlight its biochemical divergence from the human enzyme.
Edited by Myler, PJ and Fasel, NJ, 01/2008; Caister Academic Press, Norfolk, UK.
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ABSTRACT: We review how Shannon's classical notion of capacity is not enough to characterize a noisy communication channel if we intend to use that channel as a part of a feedback loop to stabilize an unstable linear system. While classical capacity is not enough, another parametric sense of capacity called "anytime capacity" is shown to be necessary for the stabilization of an unstable process. The rate required is given by the log of the system gain and the sense of reliability required comes from the sense of stability desired. A consequence of this necessity result is a sequential generalization of the Schalkwijk/Kailath scheme for communication over the AWGN channel with feedback. In cases of sufficiently rich information patterns between the encoder and decoder, we show that adequate anytime capacity is also sufficient for there to exist a stabilizing controller. These sufficiency results are then generalized to cases with noisy observations and without any explicit feedback between the observer and the controller. Both necessary and sufficient conditions are extended to the continuous time case as well. In part II, the vector-state generalizations are established. Here, it is the magnitudes of the unstable eigenvalues that play an essential role. The channel is no longer summarized by a single number, or even a single function. Instead, the concept of the anytime-rate-region is introduced in which we ask for the region of rates that the channel can support while still meeting different reliability targets for parallel bitstreams. For cases where there is no explicit feedback of the noisy channel outputs, the intrinsic delay of the control system tells us what the feedback delay needs to be while evaluating the anytime reliability of the channel.