The mechanism of cryoprotection of proteins by solutes

We have tested the capacity of 28 different compounds to protect lactate dehydrogenase from damage during freeze-thawing. These solutes come from very dissimilar chemical classes including sugars, polyols, amino acids, methylamines, and lyotropic salts. All the compounds tested, except NaCl, protected the enzyme, to varying degrees, from inactivation. The only characteristic that these compounds have in common, as a group, is that they have all been shown to be preferentially excluded from contact with the surface of proteins in aqueous solution. It has been demonstrated previously (via thermodynamic arguments) that this interaction of solutes with proteins leads to the stabilization of proteins in nonfrozen, aqueous systems. Conversely, those solutes, e.g., urea and guanidine HCl, that bind to proteins destabilize proteins in solution, and we have found that they also enhanced the inactivation of lactate dehydrogenase during freeze-thawing. Based on the results of our freeze-thawing experiments and a review of the theory of protein stabilization in nonfrozen, aqueous solution we propose that the cryoprotection afforded to isolated proteins by solutes can be accounted for by the fact that these solutes are preferentially excluded from contact with the protein's surface.     

Solute compatibility with enzyme function and structure: rationales for the selection of osmotic agents and end-products of anaerobic metabolism in marine invertebrates.

The major nitrogenous osmolytes present in the cells of marine invertebrates, notably the free amino acids glycine, alanine and proline, and trimethylamine oxide and betaine, are highly compatible with proper enzyme function and structure. These nitrogenous osmolytes display either non-perturbing or, in some cases, favorable effects on enzyme-substrate and enzyme-cofactor complex formation, catalytic velocity and protein structural stability. In contrast, inorganic salts (KCl and NaCl) and certain of the free amino acids which play only a minor osmotic role, e.g., arginine and lysine, have strongly perturbing effects on one or more of these enzymic parameters. The compatible nitrogenous solutes therefore are suitable for use at high (several tenths molar) concentrations and at widely varying concentrations in osmo-conforming species. Certain nitrogenous solutes, especially trimethylamine oxide, betaine and glutamate, offset some of the perturbing effects of inorganic ions on enzyme function. The selective accumulation of osmolytes thus involves not only the concentration of non-perturbing solutes, but also a balanced accumulation of solutes with opposing effects on enzymes. The selection of end-products of anaerobic metabolism also appears to be based, in part, on considerations of solute compatibility with enzyme function. Octopine is a non-perturbing solute, whereas arginine, which is condensed with pyruvate to form octopine, is very strongly perturbing. Succinate has marked stabilizing effects on protein structure. We conclude that the composition of the intracellular fluids of marine invertebrates reflects selection for osmolytes and end-products whose net effects create a cellular microenvironment which is conducive to optimal enzyme function and structure. The accumulation of compatible solutes may preclude the necessity for widespread changes in protein structure in adapting to concentrated or highly variable osmotic environments.     

Catalytic and structural modifications of sarcoplasmic reticulum and plasma membrane (Ca2+ + Mg2+)ATPases induced by organic solutes that accumulate in living systems

Organic solutes such as urea, methylamines, polyols and amino acid can accumulate in the cytoplasm of cells to compensate for hyperosmotic conditions in the external medium. Whereas urea is considered to be typical of solutes that destabilize structure and function of proteins, methylamines, polyols and some amino acids appear to have the opposite effect, and can also compensate for the perturbing effects of urea. These effects have been extensively analyzed for a variety of proteins in terms of global changes in enzyme structure and acceleration or inhibition of overall reaction rates. Here the influence of these solutes on sarcoplasmic reticulum and plasma membrane (Ca²⁺ + Mg²⁺)ATPases is reviewed. The focus is on the changes induced by perturbing and stabilizing solutes at specific steps of the catalytic cycles of these enzymes, which can run forward (leading to ATP hydrolysis) and backward (leading to ATP synthesis). Structural changes promoted by osmolytes are correlated with functional changes, especially those that are related to energy coupling.This review is dedicated to Prof. Carlos Chagas Filho, founder of the Institute of Biophysics, on the occasion of its 50th anniversary.     

Complementary DNA sequences of two 14.5 kDa subunits of NADH:ubiquinone oxidoreductase from bovine heart mitochondria. Completion of the primary structure of the complex?

The amino acid sequences of two nuclear-encoded subunits of complex I from bovine heart mitochondria have been determined. Both proteins have an apparent molecular weight of 14.5 kDa and their N-alpha-amino groups are acetylated. They are known as subunits B14.5a and B14.5b. Neither protein is evidently related to any known protein and their functions are obscure. A total of 34 nuclear-encoded subunits of bovine complex I have now been sequenced and it is thought that the primary structure of the complex is now complete, although with such a complicated structure it is difficult to be certain that there are no other subunits remaining to be sequenced. Seven additional hydrophobic subunits of the enzyme are encoded in mitochondrial DNA, and therefore bovine heart complex I is an assembly of about 41 different proteins. If it is assumed that there is one copy of each protein in the assembly, these polypeptides contain 7,955 amino acids in their sequences, more than are found in the Escherichia coli ribosome, which contains 7,336 amino acids in its 32 polypeptides.     

Urea and methylamine effects on rabbit muscle phosphofructokinase. Catalytic stability and aggregation state as a function of pH and temperature

The effects of urea and several methylamine solutes on the catalytic stability and aggregation properties of rabbit muscle phosphofructokinase were assessed at physiologically realistic concentrations of the solutes under several pH and temperature regimes. The loss of catalytic activity observed under conditions of pH-induced cold lability was significantly reduced in the presence of trimethylamine-N-oxide, N-trimethylglycine and N-methylglycine (order of decreasing effectiveness). The concentration-dependent methylamine stabilization of the enzyme, seen with as little as 50 mM trimethylamine-N-oxide, was accompanied by increased aggregation of the enzyme to molecular weights greater than the tetramer (polytetramer) as solute concentration was raised to 400 mM. At pH 6.5-6.7 and 25 degrees C, concentrations of urea greater than 25 mM promoted a time-dependent inactivation of the enzyme which was enhanced at lower temperatures. The urea sensitivity of the enzyme exhibited with 0.8 M urea for 1 h at pH 8.0 did not result in measurable inactivation. The fluorescence emission wavelength maximum of the enzyme was shifted to longer wavelengths and the fluorescence intensity was increased as pH was lowered to 7.0, suggesting the occurrence of a protein conformation change as specific amino acid residues of the tetramer became protonated. Measurements of enzyme light scattering indicated that perturbation by urea was correlated with tetramer dissociation, which was irreversible by dialysis at 25 degrees C. The urea and methylamine influences on phosphofructokinase activity and structure were not counteracting. The synergistic interactions among pH, temperature, and solutes observed with phosphofructokinase are compared to effects on other associating-dissociating protein systems in order to evaluate possible mechanisms of action of these low molecular weight solutes.     

Effect of poly-basic amino acids on the phosphorylation of various substrate proteins by cytosolic protein-tyrosine kinase from porcine spleen

Cytosolic protein-tyrosine kinase from porcine spleen (CPTK-40) is strongly activated by poly-L-lysine using bovine serum albumin, ovalbumin, phosphorylase b, calmodulin and H1 histone as substrate proteins. However, this polyamine inhibited the enzyme activities when myelin basic protein, tubulin and H2B histone were used as substrate proteins. These stimulatory and inhibitory effects on CPTK-40 are not specific for polylysine, but polyarginine and polyornithine have similar effects on this phosphorylation reaction. Effect of poly-basic amino acids on CPTK-40 seems to be mainly on the substrate proteins, rather than on the enzyme itself.     

Viscosity B-coefficients and standard partial molar volumes of amino acids, and their roles in interpreting the protein (enzyme) stabilization

This review systematically surveys the viscosity B-coefficients and standard partial molar volumes of amino acids at various temperatures as these data are quite important for interpreting the hydration and other properties of peptides and proteins. The effect of organic solutes and various ions on the viscometric and volumetric properties of amino acids has also been discussed in terms of their kosmotropic ('structure-making') effects on the hydration of amino acids. The comparison of these effects on the amino acid hydration enables us to have a better understanding of the influence of organic solute and salt on the protein stabilization. In addition, the viscometric and volumetric behaviors of amino acid ions (cations and anions) are also summarized because these ions have recently been incorporated as part of novel ionic liquids, which have wide applications in biocatalysis and protein stabilization.     

The 30-kilodalton subunit of bovine mitochondrial complex I is homologous to a protein coded in chloroplast DNA

In cattle, 7 of the 30 or more subunits of the respiratory enzyme NADH:ubiquinone reductase (complex I) are encoded in mitochondrial DNA, and potential genes (open reading frames, orfs) for related proteins are found in the chloroplast genomes of Marchantia polymorpha and Nicotiana tabacum. Homologues of the nuclear-coded 49- and 23-kDa subunits are also coded in chloroplast DNA, and these orfs are clustered with four of the homologues of the mammalian mitochondrial genes. These findings have been taken to indicate that chloroplasts contain a relative of complex I. The present work provides further support. The 30-kDa subunit of the bovine enzyme is a component of the iron-sulfur protein fraction. Partial protein sequences have been determined, and synthetic oligonucleotide mixtures based on them have been employed as hybridization probes to identify cognate cDNA clones from a bovine library. Their sequences encode the mitochondrial import precursor of the 30-kDa subunit. The mature protein of 228 amino acids contains a segment of 57 amino acids which is closely related to parts of proteins encoded in orfs 169 and 158 in the chloroplast genomes of M. polymorpha and N. tabacum. Moreover, the chloroplast orfs are found near homologues of the mammalian mitochondrial genes for subunit ND3. Therefore, the plant chloroplast genomes have at least two separate clusters of potential genes encoding homologues of subunits of mitochondrial complex I. The bovine 30-kDa subunit has no extensive sequences of hydrophobic amino acids that could be folded into membrane-spanning alpha-helices, and although it contains two cysteine residues, there is no clear evidence in the sequence that it is an iron-sulfur protein.     

Trimethylamine-N-oxide counteracts urea effects on rabbit muscle lactate dehydrogenase function: a test of the counteraction hypothesis.

Trimethylamine-N-oxide (TMAO) in the cells of sharks and rays is believed to counteract the deleterious effects of the high intracellular concentrations of urea in these animals. It has been hypothesized that TMAO has the generic ability to counteract the effects of urea on protein structure and function, regardless of whether that protein actually evolved in the presence of these two solutes. Rabbit muscle lactate dehydrogenase (LDH) did not evolve in the presence of either solute, and it is used here to test the validity of the counteraction hypothesis. With pyruvate as substrate, results show that its Km and the combined Km of pyruvate and NADH are increased by urea, decreased by TMAO, and in 1:1 and 2:1 mixtures of urea:TMAO the Km values are essentially equivalent to the Km values obtained in the absence of the two solutes. In contrast, values of k(cat) and the Km for NADH as a substrate are unperturbed by urea, TMAO, or urea:TMAO mixtures. All of these effects are consistent with TMAO counteraction of the effects of urea on LDH kinetic parameters, supporting the premise that counteraction is a property of the solvent system and is independent of the evolutionary history of the protein.     

Significant role of the nitrogen recycling system through the ceca occurs in protein-depleted chickens

This study focuses on the role of the ceca in nitrogen nutrition in chickens (Gallus domesticus). Urea is a very good nitrogen tracer for these studies. Little urea is synthesized by chickens due to the absence of carbamyl phosphate synthetase, an essential enzyme initiating the urea cycle. Urea is utilized by chickens when crystalline amino acid diets low in nonessential nitrogen or diets containing low concentrations of intact protein are fed, and most ureolytic activity is found in the ceca. Dietary urea was absorbed intact from the upper intestine of the chicken. The absorbed urea was excreted into ureteral urine that refluxed from the cloaca into the colon and ceca where urea was degraded to ammonia. Presumably the ammonia was incorporated into amino acids by cecal microorganisms and some urea, amino acids and proteins were absorbed from the ceca. These were utilized by the chickens. A beneficial role of ceca in the nitrogen metabolism in the chicken is, therefore, conservation of urinary nitrogen in protein-depleted chickens.     

Hypochlorous acid-mediated protein oxidation: how important are chloramine transfer reactions and protein tertiary structure?

Hypochlorous acid (HOCl) is a powerful oxidant generated from H2O2 and Cl- by the heme enzyme myeloperoxidase, which is released from activated leukocytes. HOCl possesses potent antibacterial properties, but excessive production can lead to host tissue damage that occurs in numerous human pathologies. As proteins and amino acids are highly abundant in vivo and react rapidly with HOCl, they are likely to be major targets for HOCl. In this study, two small globular proteins, lysozyme and insulin, have been oxidized with increasing excesses of HOCl to determine whether the pattern of HOCl-mediated amino acid consumption is consistent with reported kinetic data for isolated amino acids and model compounds. Identical experiments have been carried out with mixtures of N-acetyl amino acids (to prevent reaction at the alpha-amino groups) that mimic the protein composition to examine the role of protein structure on reactivity. The results indicate that tertiary structure facilitates secondary chlorine transfer reactions of chloramines formed on His and Lys side chains. In light of these data, second-order rate constants for reactions of Lys side chain and Gly chloramines with Trp side chains and disulfide bonds have been determined, together with those for further oxidation of Met sulfoxide by HOCl and His side chain chloramines. Computational kinetic models incorporating these additional rate constants closely predict the experimentally observed amino acid consumption. These studies provide insight into the roles of chloramine formation and three-dimensional structure on the reactions of HOCl with isolated proteins and demonstrate that kinetic models can predict the outcome of HOCl-mediated protein oxidation.     

Distinct sequence determinants direct intracellular sorting and modification of a yeast vacuolar protease

We have mapped a sequence determinant in the vacuolar glycoprotein carboxypeptidase Y (CPY) that directs intracellular sorting of this enzyme. Through the study of hybrid proteins, consisting of amino-terminal segments of CPY fused to the secretory enzyme invertase, we have found that the N-terminal 50 amino acids of CPY are sufficient to direct delivery of a CPY-Inv hybrid protein to the yeast vacuole. Our data suggest that this 50 amino acid segment of CPY contains two distinct functional domains; an N-terminal signal peptide followed by a segment of 30 amino acids that contains the vacuolar sorting signal. Deletion of this putative vacuole sorting signal from an otherwise wild-type CPY protein leads to missorting of CPY. Furthermore, examination of the Asn-linked oligosaccharides present on CPY and CPY-Inv hybrid proteins suggests that an additional determinant in CPY specifies the extent to which these proteins are glycosylated in the Golgi complex.     

Role of adenosine monophosphate in regulation of metabolic pathways of perfused rat liver

1. By perfusion of rat livers with 3mm-AMP in the perfusion medium we obtain increased intracellular concentrations of AMP. 2. These high intracellular concentrations of AMP lead to an increased output of glucose and urea into the perfusion medium. 3. The increased output of glucose in livers from fed rats is brought about primarily by an AMP-stimulated breakdown of liver glycogen. In livers from starved rats the increase in glucose output is not as great, reflecting the low contents of glycogen in livers from starved rats. 4. AMP inhibits gluconeogenesis from lactate in perfused livers. In the presence of high concentrations of lactate, however, the counteracting effects of AMP to increase glycogenolysis and to inhibit gluconeogenesis result in little change in the net glucose output. 5. The increased urea output is brought about by increased breakdown of amino acids that are present in the perfusion medium. In livers from starved rats the overall urea production is much higher, indicating increased catabolism of amino acids and other nitrogenous substrates in the absence of carbohydrate substrates. 6. AMP causes an inhibition of incorporation of labelled precursors into protein and nucleic acid. This may result from increased catabolism of precursors of proteins and nucleic acids as reflected by the more rapid breakdown of nitrogenous compounds. In support of this hypothesis, cell-free systems for amino acid incorporation isolated from livers perfused with and without AMP are equally capable of supporting protein synthesis. 7. The labelling pattern of RNA in perfused livers corresponds very closely to those found by pulse-labelling in vivo. AMP in no way alters the qualitative nature of the labelling patterns. 8. We consider these results as supporting evidence for the role of the concentration ratio of AMP to ATP in controlling the metabolic pathways that lead to the formation of ATP.     

Complete and partial glycophospholipid anchors are found on a fusion protein consisting of luteinizing hormone beta subunit followed by a carboxyl-terminal domain of Thy-1.

The Thy-1 antigen is anchored to the cell surface by a carboxyl-terminal glycophospholipid moiety. To investigate the extent of anchor addition which occurs when such proteins cannot move efficiently to the cell surface, we have expressed a recombinant fusion protein composed of 107 amino-terminal amino acids of bovine luteinizing hormone beta subunit and 46 COOH-terminal amino acids of murine Thy-1 (Thy-1.2 allele). Although the limited amount of fusion protein transported to the cell surface is glycophospholipid-anchored, most of the protein accumulates in an intracellular, endoglycosidase H-sensitive form. The intracellular protein has an unusual structure that contains ethanolamine but does not bind detergent, suggesting either that anchor addition proceeds via a hydrophilic partial intermediate, or that anchor-degradative enzymes exist along the secretory path.     

Suppression of protein interactions by arginine: a proposed mechanism of the arginine effects

Arginine has been used to suppress protein aggregation and protein-protein or protein-surface interactions during protein refolding and purification. While its biotechnology applications are gradually expanding, the mechanism of these effects of arginine has not been fully elucidated. Arginine is more effective at higher concentrations, an indication of weak interactions with the proteins. The effects of weakly interacting additives, such as arginine, on protein solubility, stability and aggregation have been explained from three different approaches: i.e., (1) the effects of additives on the structure of water, (2) the interactions of additives with the amino acid side chains and peptide bonds and (3) the preferential interactions of additives with the proteins. Here we have examined these properties of arginine and compared with those of other additives, e.g., guanidine hydrochloride (GdnHCl) and certain amino acids and amines. GdnHCl is a strong salting-in agent and denatures proteins, while betaine is a protein stabilizer. Several amino acids and amine compounds, including betaine, which stabilize the proteins, are strongly excluded; i.e., the proteins are preferentially hydrated in these solutions. On the other hand, GdnHCl preferentially binds to the proteins. Arginine is intermediate between these two extreme cases and shows a more complicated pattern of interactions with the proteins. The effects of additives on water structure, e.g., the surface tension of aqueous solution of the additives and the solubility of amino acids in the presence of additives also shed light on the mechanism of the effects of the additives on protein aggregation. While arginine increases the surface tension of water, it favorably interacts with most amino acid side chains and the peptide bonds, a property shared with GdnHCl. Thus, we propose that while arginine is similar to GdnHCl in the amino acid level, arginine interacts with the proteins differently from GdnHCl.     

Solute effects on mitochondria from an elasmobranch (Raja erinacea) and a teleost (Pseudopleuronectes americanus)

Varying osmolarity with sucrose/KCl media resulted in similar effects on the oxidation of glutamate by mitochondria isolated from the livers of an elasmobranch, Raja erinacea, and a teleost, Pseudopleuronectes americanus. In both species trimethylamine oxide (TMAO) inhibited mitochondrial oxidation of glutamate. Urea penetrated the inner mitochondrial membrane of both species and equilibrated with a ratio ureai/ureao of unity. Urea had little effect on the oxidation of glutamate in both species at concentrations as high as 760 mM. Addition of urea (urea/TMAO, 2:1) did not overcome the detrimental effects of TMAO in the mitochondria of either species. In the case of the elasmobranch, the osmolarity of the urea/TMAO media giving the optimal rate of respiration was hypoosmotic with respect to the intracellular osmolarity. The rate of glutamate oxidation steadily declined as osmolarity increased above this value. Assuming the osmotic profile obtained with the urea/TMAO (2:1) medium resembled most closely the in vivo situation, higher rates of oxidation or organic solutes at low osmolarity would help deplete the cell of these solutes and could contribute to cell volume regulation during hypoosmotic stress. It is suggested that two broad classes of intracellular solutes can be defined based on their effects on mitochondrial respiration. Solutes such as K+, C1-, and TMAO penetrate the inner mitochondrial membrane slowly or not at all. Increasing concentrations of these solutes result in lower rates of oxidation. This capacity may be important in regulating intracellular levels of organic solutes during osmotic stress. Solutes such as urea rapidly penetrate the cell and inner mitochondrial membrane reducing the mitochondrial volume changes associated with osmotic stress. The known detrimental effects of urea on protein structure may prevent its exclusive use as an intracellular osmotic effector.     

Requirement of transmembrane transport for S-nitrosocysteine-dependent modification of intracellular thiols

S-nitrosothiols have been implicated as intermediary transducers of nitric oxide bioactivity; however, the mechanisms by which these compounds affect cellular functions have not been fully established. In this study, we have examined the effect of S-nitrosothiol transport on intracellular thiol status and upon the activity of a target protein (caspase-3), in bovine aortic endothelial cells. We have previously demonstrated that the specific transport of amino acid-based S-nitrosothiols (S-nitroso-L-cysteine and S-nitrosohomocysteine) occurs via amino acid transport system L to generate high levels of intracellular protein S-nitrosothiols (Zhang, Y., and Hogg, N. (2004) Proc. Natl. Acad. Sci. U. S. A. 101, 7891-7896). In this study, we demonstrate that the transport of S-nitrosothiols is essential for these compounds to affect intracellular thiol levels and to modify intracellular protein activity. Importantly, the ability of these compounds to affect intracellular processes occurs independently of nitric oxide formation. These findings suggest that the major action of these compounds is not to liberate nitric oxide in the extracellular space but to be specifically transported into cells where they are able to modify cellular functions through nitric oxide-independent mechanisms.     

ATP synthase from bovine mitochondria: sequences of imported precursors of oligomycin sensitivity conferral protein, factor 6, and adenosinetriphosphatase inhibitor protein

Oligomycin sensitivity conferral protein (OSCP), factor 6 (F6), and ATPase inhibitor protein are all components of the ATP synthase complex of bovine mitochondria. They are encoded in nuclear DNA. Complementary DNA clones encoding the precursors of these proteins have been isolated from a bovine library by using mixtures of synthetic oligonucleotides as hybridization probes, and their DNA sequences have been determined. The deduced protein sequences show that the OSCP, F6, and inhibitor proteins have N-terminal presequences of 23, 32, and 25 amino acids, respectively. These presequences are not present in the mature proteins. It is assumed that they serve to direct the proteins into the mitochondrial matrix. The cDNA clones have also been employed as hybridization probes to investigate the genetic complexity of the three proteins in cows and humans. These experiments indicate that the bovine and human inhibitor and bovine F6 proteins are encoded by single genes but suggest the possibility of the presence in both species of more than one gene (or pseudogenes) for the OSCP.     

Glucosylglycerol and glucosylglycerate as enzyme stabilizers

Compatible solutes constitute a diverse class of low-molecular-mass organic molecules that are accumulated in high intracellular concentrations in response to the external stress of hyperosmolality or high temperature. Many of these compounds like α, α-trehalose are well known for their stabilizing effect on protein structure and could lead to development of more stable protein formulations. Negatively charged solutes like mannosylglycerate (R-2-O-α-D -mannopyranosyl-glycerate) are widespread among (hyper)thermophilic microorganisms and are thought to be exceptionally potent stabilizers of proteins under high-temperature denaturation conditions. To further inquire into the role of compound charge for protective function, we have compared two naturally occurring and structurally related solutes, glucosylglycerol (2-O-α-D -glucopyranosyl-sn-glycerol) and glucosylglycerate (R-2-O-α-D -glucopyranosyl-glycerate), as stabilizers of different enzymes undergoing inactivation through elevated temperature or freeze drying, and benchmarked their effects against that of α,α-trehalose. Glucosylglycerate in concentrations of ≥0.1 M was the most effective in preventing thermally induced loss of enzyme activity of lactate dehydrogenase, mannitol dehydrogenase, starch phosphorylase, and xylose reductase. α,α-Trehalose could usually be replaced by glucosylglycerol without compromising enzyme stability. Glucosylglycerol and glucosylglycerate afforded substantial (eightfold) protection to mannitol dehydrogenase during freeze drying.