Protein functional group

Functional group protein Functional group surface binding... 

Protein functional groups able to react with anhydrides include the oc-amines at the N-terminals, the s-amine of lysine side chains, cysteine sulfhydryl groups, the phenolate ion of tyrosine residues, and the imidazolyl ring of histidines. However, acylation of cysteine, tyrosine, and histidine side chains forms unstable complexes that are easily reversible to regenerate the original group. Only amine functionalities of proteins are stable to acylation with anhydride reagents (Fraenkel-Conrat, 1959 Smyth, 1967). 

The relative reactivity of a-haloacetates toward protein functional groups is sulfhydryl > imidazolyl > thioether > amine. Among halo derivatives the relative reactivity is I > Br > Cl > F, with fluorine being almost unreactive. The oc-haloacetamides have the same trend of relative reactivities, but will create a terminal amide group not a terminal carboxylate. 

Under certain conditions, such as conformational restrictions or absence of any better acceptors, carbon-bound fluorine presumably accepts hydrogen bonds from protein functional groups (Section 2.2.1). 

Where this factor plays a role, the hydrophobic interaction between the hydrocarbon chains of the surfactant and the non-polar parts of protein functional groups are predominant. An example of this effect is the marked endothermic character of the interactions between the anionic CITREM and sodium caseinate at pH = 7.2 (Semenova et al., 2006), and also between sodium dodecyl sulfate (SDS) and soy protein at pH values of 7.0 and 8.2 (Nakai et al., 1980). It is important here to note that, when the character of the protein-surfactant interactions is endothermic (/.< ., involving a positive contribution from the enthalpy to the change in the overall free energy of the system), the main thermodynamic driving force is considered to be an increase in the entropy of the system due to release into bulk solution of a great number of water molecules. This entropy... 

Protein functional groups able to react with anhydrides include the a-amines at the... 

H. R. Costantino, K. Griebenow, R. Danger, and A. M. Klibanov, On the pH memory of lyophilized compounds containing protein functional groups, Biotechnol. Bioeng. 1997, 53, 345-348. 

There are no published studies which examine the significance of pH shifts on quality attributes of freeze-dried formulations of small molecules. However, Costantino et al. (14) reported that lyophilized organic compounds containing protein functional groups (amino-, carboxylic-, and phenolic-) exhibit pH memory that is, the ionization state of the solid, as reflected by the FTIR spectrum, is similar to that of the aqueous solution from which the compound was freeze dried. 

VI. SPECIFIC BACTERIA USING AMINO ACIDS AND PROTEIN FUNCTIONAL GROUPS OF HETEROTROPHIC BACTERIA... 

One of the major drawbacks of the diazoacetyl group was its instability at low pH and its reactivity in the dark towards protein functional groups (see Section 4.7.2). The 2-diazo-3,3,3-trifluoropropionyl and p-toluenesul-fonyldiazoacetyl groups are considerably improved in these respects and are stable in 1 M hydrochloric acid. 

The principle advantage of the physical labeling method is the possibility of receiving direct information about the structure, mobility and local micropolarity of certain parts of a molecular object of any molecular mass. Developments in synthetic chemistry, biochemistry and site-directed mutagenesis have provided researchers with a wide assortment of labels and probes, and have paved the way for the specific modification of protein function groups, including enzyme active sites. 

Water molecules are small probes. They can hydrogen-bond to protein functional groups with few steric limitations, in contrast to the hydrogen bonds between protein main-chain and side-chain atoms which have been the topic of Part III, Chapter 19. The hydrogen bonds involving water are therefore considered to reflect the intrinsic hydrogen-bonding properties of a protein. 

Iteble 23.5. Metrical analysis of hydrogen bonds between water molecules and protein functional groups. The data are taken from the 15 protein crystal structures with water positions located, see Tkble 19.1, Part III, and [596]. Compare with Fig. 23.5 with somewhat different sampling... 

Krull, H., and Friecbnan, M. (1967). Anionic polymerization of methyl acrylate to protein functional groups. J. Polym. Sci. A-l, 5, 2535-2546. 

Early experiments with bacteriorhodopsin (228) interpreted the Raman spectrum in terms of an unprotonated Schiff base, forming a charge-transfer complex with a protein functional group (210,212). This interpretation of the Raman data, essentially based on a comparison with the frequencies of model Schiff bases in solution, was criticized by Honig and Ebrey (48), who pointed out that consistency could also be obtained with a protonated Schiff base model. The latter hypothesis was subsequently confirmed by deuteration experiments similar to those described for rhodopsin (229,230), and by Raman spectra in denatured systems (231). In variance with the clear-cut similarity observed between the resonance-Raman spectra of rhodopsin and isorhodopsin, and those of the 11-cis and 9-cis model compounds, respectively,... 

Optical Spectra. The main (a) band in a variety of visual pigments exhibits absorption maxima in the range between 430 and 580 nm. It is this variability, as well as the basic bathochromic shift relative to a free PRSB in solution, which have provided the basis for most of the spectroscopic theories relevant to the structure of the chromophore and its environment in the binding site. Attempts to rationalize the shift in terms of charge-transfer complex formation between the (unprotonated) Schiff base and a protein functional group (200,210,212,228) have never... 

Conjugation reagents bind to protein functional groups NHj-, SH-, OH-, phenol, etc. Reagents which react with the amino groups are usually preferred. The utilization of SH-groups could be risky because they can be included in the catalytic site of an enzyme or participate in some other way in the biological activity of protein to be labeled protein cannot occur. The presence of a radiolabel outside of the peptide active site. 

These considerations form the basis for the numerous techniques that are now available for the chemical modification of proteins. The sections that follow will examine these techniques and the reactive principles by which they function. A section describing reactions that display orthogonal reactivity to native protein functional groups has also been included because of the growing importance of these reactions as tools to label proteins in complex mixtures. Because it is not practical to summarize all protein bioconjugation methods here, this information instead is intended to serve as an introduction to the concepts that drive the development of these reactions. Several additional reviews and books on protein modification have been listed in the Further Reading section. 

Constantino HR, Griebenow K, Danger R, and Klibanov AM. On the pH Memory of Lyophilized Compounds Containing Protein Functional Groups. Biotechnol Bioengl991 53 345-348. 

For efficient transport of relatively insoluble CO2 from the tissues where it is formed to the lungs where it must be exhaled, the buffers of the blood convert CO2 to the very soluble anionic form HCOJ (bicarbonate ion). The principal buffers in blood are bicarbonate-carbonic acid in plasma, hemoglobin in red blood cells, and protein functional groups in both. The normal balance between rates of elimination and production of CO2 yields a steady-state concentration CO2 in the body fluids and a relatively constant pH. 

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