Single protein

Semi-empirical methods could thus treat the receptor portion of a single protein molecule as a quantum mechanical region but ab mdio methods cannot. However, both semi-empirical and ab initio methods could treat solvents as a perturbation on a quantum mechanical solute. In the future, HyperChem may have an algorithm for correctly treating the boundary between a classical region and an ab mdio quantum mechanical region in the same molecule. For the time being it does not. 

A nucleic acid can never code for a single protein molecule that is big enough to enclose and protect it. Therefore, the protein shell of viruses is built up from many copies of one or a few polypeptide chains. The simplest viruses have just one type of capsid polypeptide chain, which forms either a rod-shaped or a roughly spherical shell around the nucleic acid. The simplest such viruses whose three-dimensional structures are known are plant and insect viruses the rod-shaped tobacco mosaic virus, the spherical satellite tobacco necrosis virus, tomato bushy stunt virus, southern bean mosaic vims. 

FIGURE 5.23 Electrospmy mass spectrum of the protein, aerolysin K. The attachment of many protons per protein molecule (from less than 30 to more than 50 here) leads to a series of m/z peaks for this single protein. The inset shows a computer analysis of the data from this series of peaks that generates a single peak at the correct molecular mass of the protein. (Adapted from Figure 2 in Mann, M., and Wilm, M., 1995. Trends in Biochemical Sciences 20 219-224.)... 

The tertiary structure - the spatial arrangement of all of the amino acids in a single protein chain, i.e. the three-dimensional structure of the protein. 

It is not practical to sequence more than about 50 amino acid residues on a single protein in this way and larger proteins need to be broken down into polypeptides with more appropriate lengths to allow complete sequencing to be carried out. This shortening of the polypeptide chain may be carried out using chemical or enzymatic methods, cf. hydrolysis. 

FIG. 3 Three-dimensional model of the protein mass distribution of the S-layer of Bacillus stearothermophilus NRS 2004/3a [(a) outer, (b) inner face]. The square S-layer is about 8 nm thick and exhibits a center-to-center spacing of the morphological units of 13.5 nm. The protein meshwork composed of a single protein species shows one square-shaped, two elongated, and four small pores per morphological unit. (Modified from Ref. 7.)... 

A step closer toward realism is taken by off-lattice models in which the backbone is specified in some detail, while side chains, if they are represented at all, are taken to be single, unified spheres [44-50]. One indication that this approach is too simplistic was given in [51], which proved that for a backbone representation in which only Ca carbons were modeled, no contact potential could stabilize the native conformation of a single protein against its nonnative ( decoy ) conformations. However, Irback and co-workers were able to fold real protein sequences, albeit short ones, using a detailed backbone representation, with coarse-grained side chains modeled as spheres [49, 52-54]. 

As stated above, the most important missing piece in protein folding theory is an accurate all-atom potential. Recently there has been much effort in this direction, and much more is needed [48,55,72-77]. The existence of a potential satisfying minimal criteria such as folding and stability for a single protein was demonstrated in [73]. It is not a realistic potential by any means, but its existence validates the all-atom, implicit solvent, Monte Carlo approach as a serious candidate for theory. The method used to derive this potential was ad hoc, and has recently been compared with other standard methods in a rigorous and illuminating study [77]. 

Purified membrane proteins or enzymes can be incorporated into these vesicles in order to assess what factors (eg, specific lipids or ancillary proteins) the proteins require to reconstitute their function. Investigations of purified proteins, eg, the Ca " ATPase of the sarcoplasmic reticulum, have in certain cases suggested that only a single protein and a single lipid are required to reconstitute an ion pump. 

The five enzyme activities are localized in the microsomal fraction in rat testes, and there is a close functional association between the activities of 3P-OHSD and A -isomerase and between those of a 17oc-hydroxylase and 17,20-lyase. These enzyme pairs, both contained in a single protein, are shown in the general reaction sequence in Figure 42-5. 

Figure 42-5. Pathways of testosterone biosynthesis. The pathway on the left side of the figure is called the or dehydroepiandrosterone pathway the pathway on the right side is called the A" or progesterone pathway. The asterisk indicates that the 17a-hydroxy-lase and 17,20-lyase activities reside in a single protein, P450cl7.

Single protein kinases such as PKA, PKC, and Ca +-calmodulin (CaM)-kinases, which result in the phosphorylation of serine and threonine residues in target proteins, play a very important role in hormone action. The discovery that the EGF receptor contains an intrinsic tyrosine kinase activity that is activated by the binding of the hgand EGF was an important breakthrough. The insuhn and IGF-I receptors also contain intrinsic... 

Actinia cari. When an extract of the tentacles of this species was subjected to gel nitration, a single protein peak having hemolytic and lethal activities was obtained. Further fractionation by CM-cellulose ion-exchange chromatography yielded three well separated peaks (CTl, Cmi, Cmil) which appeared to be similar in biological activity (14). 

Complement is not a single protein but comprises a group of functionally linked proteins that interact with each other to provide mar of the effector functions of humoral immunity and inflammation. Most of the components of the system are present in the serum as proenzymes, i.e. enzyme precursors. Activation of a complement molecule occurs as a result of proteolytic cleavage of the molecule, which in itself confers proteolytic activity on the molecule. Thus, many components of the system serve as the substrate of a prior component and, in turn, activate a subsequent component. This pattern of sequential activation results in the system being called the complement cascade. ... 

Separation of the purified PL1, PL2 and PL3 isoenzymes by SDS-PAGE yielded single protein bands that corresponded to a molecular mass of 42 kDa (6), 4 kDa higher than calculated from the deduced amino acid sequences. Isoelectric focusing revealed a pi of >10 for each isoenzyme similar to that of the basic Ech PLs (15). 

The fact that no mutation outside the cloned locus is known to inactivate the same transport system also favours the idea that, in each case, the transporter is a single protein. 

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