Test of the extended two-state model for the kinetic intermediates observed in the folding transition of ribonuclease A

A test has been made of the proposal that: (a) the extended two-state model describes the kinetic intermediates seen in the folding transition of RNAase A, i.e. that the only species present in folding experiments are the native protein and multiple forms of the completely unfolded protein; and (b) that the interconversion between the two known unfolded forms of RNAase A (the U₁

U₂ reaction) is described solely by the cis-trans isomerization of the proline residues. The test is to measure the rate of the U₁

U₂ reaction in a wide range of refolding conditions and to compare these data with the kinetic properties of proline isomerization.The main results are as follows. (1) The activation enthalpy of the U₁

U₂ reaction in refolding conditions (pH 6, 20 ° to 40 °C) is less than 5 kcal/mol. This is much too small to be explained as proline isomerization. (2) Both the rate and the activation enthalpy change sharply at guanidine hydrochloride concentrations below 2 m. There appear to be two pathways for the U₁

U₂ reaction in refolding conditions, and the slower pathway is favored by adding guanidine hydrochloride. (3) The rate and activation enthalpy for proline isomerization in l-alanyl-l-proline are unaffected by 2 m-guanidine hydrochloride.The results show that the proline isomerization hypothesis and the extended two-state model cannot both be correct for RNAase A. They suggest that partial folding occurs rapidly in refolding conditions and that the extended two-state model is invalid. They leave open the question of whether or not proline isomerization is the rate-limiting step in the U₁

U₂ reaction.Another possible source of slow configurational reactions in the unfolded state is mentioned. The three major, overlapping, disulfide-bonded loops of RNAase A can exist in two isomeric configurations. Interconversion of these isomers requires pulling one loop, or one end of the polypeptide chain, through a second loop and this is likely to be a slow process.In some conditions, heat-unfolded but not guanidine-unfolded RNAase A shows a second slow-refolding process. It may result from aggregates of the heatunfolded protein which are formed and broken up slowly. Conditions are given for eliminating this reaction.     

Unfolding and refolding of the reduced constant fragment of the immunoglobulin light chain: Kinetic role of the intrachain disulfide bond

The constant fragment of the immunoglobulin light chain whose intrachain disulfide bond is reduced (reduced C_L fragment) assumes a conformation very similar to the intact C_L fragment (Goto & Hamaguchi, 1979). The kinetics of reversible unfolding and refolding of the reduced C_L fragment by guanidine hydrochloride at pH 7.5 and 25 °C were studied and were compared with those of the intact C_L fragment described in the accompanying paper (Goto & Hamaguchi, 1982). Tryptophyl fluorescence, far-ultraviolet circular dichroism, and reactivity of the SH groups toward 5,5′-dithiobis-(2-nitrobenzoic acid) were used to follow the kinetics. The results obtained were thoroughly explained on the basis of the three-species mechanism, U₁

U₂

N, where U₁ and U₂ are slow-folding and fast-folding species, respectively, of unfolded protein and N is native protein. The rate constants of interconversion between U₁ and U₂ and the rate constant for the process from N to U₂ were very similar to the respective values for the intact C_L fragment. Only the rate constant for the process from U₂ to N was greatly different between the intact and reduced C_L fragments; the rate constant for the reduced C_L fragment was about 100 times smaller than that for the intact C_L fragment. These results indicated that the slow isomerization of the unfolded molecule is independent of the presence of the disulfide bond and that the kinetic role of the intrachain disulfide bond is to accelerate the folding process. This kinetic role in the folding of the C_L fragment was explainable only in terms of the decreased entropy in the unfolded state of the intact C_L fragment due to the presence of the disulfide bond.     

The effect of tin chloride on the structure and function of dna in human white blood cells

Tin compounds are being used increasingly in

in industry and in medicine. There have been relatively few studi

ng term biological effects of this metal, although acute effects h

cumented. In this report we describe experiments which show tha

stannous chloride, is readily taken up by human white blood cells

an cause damage to DNA. Damage was detected in WBC after e

-50 μM tin(II) for 30 min at either 0°C or 37°C. The amount o

served was more extensive than that produced by exposure of

nolar amounts of chromium(VI), a known carcinogen and DNA

agent. Additional indication of cellular damage is that exposm

n lymphocytes or mouse splenocytes to tin(II) interfered with thei

o be stimulated by the polyvalent mitogen concanavalin A (Con A).

rast, tin(IV) was not taken up by cells, did not cause DNA damage nor d

inhibit stimulation of DNA synthesis in cells that were exposed to Con A.     

Nonenzymic hydrolysis of ATP–infrared investigations of intermolecular interactions

The nonenzymic hydrolysis of

and

were studied by infrared (IR) spectroscopy. Protons resulting from hydrolysis of ATP are not bound to the N₁ atoms of the adenine residues. With hydrolysis of

, these protons are partially bound to the terminal phosphate group of ADP, namely,

,

,

, and

, present after hydrolysis. With decreasing pH or when Mg²⁺ ions are present, all hydrolysis protons are attached to the orthophosphate molecules.With hydrolysis of

the pH decreases up to 40% degree of hydrolysis. Then the system becomes self-buffered in the physiological pH region. A similar pH decrease is found with hydrolysis of

. With these systems, however, the pH decreases slightly also at degrees of hydrolysis larger than 40%. No other systems show pronounced pH changes during hydrolysis; in other words, they are buffer systems.The IR bands demonstrate that mesomeric bond resonance in the phosphate groups strongly depends on whether protons are present at these groups. Regarding the equilibria of proton attachment mentioned above, mesomeric bond resonance in these groups strongly depends on pH and on the presence of

ions.With hydrolysis of ATP, two POH groups are formed that bind H₂O molecules via strong hydrogen bonds, changing the solvate structure. Finally, easily polarizable hydrogen bonds are formed, for instance,

bonds with the hydrolysis of

, and

bonds with the hydrolysis of

. These bonds strongly interact with their environment. The formation of these hydrogen bonds strongly depends on pH and the presence of

ions.All these effects, especially the intermolecular ones, contribute to the change of free energy during ATP hydrolysis.     

Studies of the self-association of bacteriophage T4 gene 32 protein by equilibrium sedimentation.

The self-association of the bacteriophage T4 gene 32 protein has been examined in the analytical ultracentrifuge under varying conditions to determine the nature of the process. The process is not a simple indefinite association with one association constant (monomer

dimer

trimer

etc.). The complexity of the process is shown by (1) peculiarities in the molecular weight versus concentration curves, in the region of the dimer (observed with increasing ionic strength, at pH 10, in 0.04 m-MgCl₂, with aged preparations, at 19 °C and in the presence of the oligonucleotide d(pT)₁₀), (2) the increased sigmoidicity of the association curve in the presence of glycerol or oligo[d(pT)₄], and (3) the discontinuity in the association curve at the tetramer at a pH value of approximately 9.4. A model with two association constants which could vary independently (monomer

dimer

tetramer

etc.) explained many of the findings. However, a more complex model was required to explain curves which had a plateau at the dimer with increased association at higher protein concentrations. Thus, under all conditions examined there is evidence for more than one type of protein-protein interaction. These different interactions may be involved in a physiological function such as recombination.     

A survey of hydrogen bond geometries in the crystal structures of amino acids

An analysis of the geometries of the hydrogen bonds observed by neutron diffraction in thirt-two crystal structures of amino acids shows the following results. Of the 168 hydrogen bonds in the data set, 64 involve the zwitterion groups 

and $\text{C}$O₂. Another 18 are from

to sulphate or carbonyl oxygens. The majority, 46, of these

H … O bonds are three-centered (bifurcated). Nine are four-centered (trifurcated). The geometry in which the three-centered hydrogen bond involves both oxygens of the same carboxylate group is not especially favoured. When it does occur, one hydrogen bond is generally shorter and the other longer, than when the bonding involves oxygens on different carboxylate groups. The shortest hydrogen bonds are the OH … O $\text{C}$, from a carboxylic acid hydroxyl to a carboxylate oxygen, and NH … O$\text{C}$ when the nitrogen is the ring atom in histidine or proline. Carboxylate groups, on average, accept six hydrogen bonds, with no examples of less than four bonds. The reason for the large number of three-centered

H … O$\text{C}$ bonds is therefore a proton deficiency arising from the disparity between the tripled donor property of the

groups and the sextuple, on average, acceptor property of the carboxylate groups. There is good geometrical evidence for the existence of H … O and H … Cl^? hydrogen bonds, especially involving the hydrogen atoms on α-atoms.     

Reaction kinetics of P-700, cytochrome c-553 and cytochrome f in the cyanobacterium, Synechococcus sp

Absorption changes invoked by short flashes in the Soret band region were measured in the thermophilic cyanobacterium Synechococcus sp. and photoresponses of P-700, cytochrome c-553 and cytochrome f were resolved with the aid of a microcomputer. Cytochrome c-553 was oxidized very rapidly with a half-time of less than 20 μs, while the half oxidation time of cytochrome f was 35–45 μs. The two cytochromes were reduced monophasically with half-time of 2 ms after a lag lasting a few milliseconds. The reduction kinetics of P-700 showed three exponential phases with half-times of 40 μs, 200 μs and 2 ms, which are ascribed to electron donation from cytochrome f, the Rieske iron-sulfur protein and plastoquinone, respectively. The results support the following sequence and rates of linear electron transport at the physiological temperature of the cyanobacterium: P-700

cytochrome c-553

cytochrome f

Rieske protein

plastoquinone.     

Genetic and sequence analysis of frameshift mutations induced by ICR-191

A genetic and sequence analysis of 373 ICR-191-induced mutations in the lacI gene of Escherichia coli reveals that 365 of the mutations (97·9%) are frameshifts involving the addition or deletion of a single

base-pair from a

sequence including, in one case, a

sequence. Some of the remaining eight mutations (2·1%) represent the loss or gain of a

base-pair from a

sequence. Certain mutational sites are relative hotspots for ICR-191-induced mutations, and we have analyzed the role of surrounding sequences on relative mutation rates. The preference for +1 frameshifts or ?1 frameshifts is site-specific, so that at some sites +1 frameshifts predominate by a 10:1 ratio, whereas at other sites ?1 frameshifts are favored by an approximately 2:1 ratio. The characterized frameshift mutations in lacI described here are useful for constructing systems to detect other frameshift and deletion mutations.     

Cytochrome f and plastocyanin kinetics in Chlorella pyrenoidosa. I. Oxidation kinetics after a flash

P-700, plastocyanin and cytochrome f redox kinetics were measured after one flash, using dark-adapted Chlorella in the presence of hydroxylamine and 3(3,4-dichlorophenyl)-1,1-dimethylurea. Plastocyanin becomes increasingly oxidized with a half-time of 70 μs, then undergoes reduction with a half-time of 7 ms. Cytochrome f oxidation has a sigmoidal time-course and a half-time of 100 μs. Its reduction exhibits a half-time of 4 ms. These results are interpreted in a linear scheme:

An equilibrium constant of 2 between cytochrome f and plastocyanin (PC), which contrasts with the large equilibrium constant between PC and P-700 is computed.The presence of cytochrome b₆ in a cyclic path around Photosystem I is confirmed under these conditions.     

Pyruvate carboxylase: Mechanism of the second partial reaction

The stoichiometry of the products of the pyruvate carboxylase reaction has been investigated and shown to vary as the concentration of pyruvate was altered. At high concentrations of pyruvate, the ratio of orthophosphate liberated to oxaloacetate produced approached one, but as the pyruvate concentration was decreased, the ratio increased. On the basis of this evidence, a model for the reaction mechanism was proposed in which the

complex could react either with pyruvate to form oxaloacetate, or water to produce

and HCO₃^?. The nonproductive breakdown of the enzyme-substrate complex and the resulting lack of stoichiometry provides an explanation for the nonlinear double reciprocal plots obtained for both the overall reaction and the pyruvate:oxaloacetate exchange reaction. Since neither the rate of breakdown of the isolated

complex nor the rate of decarboxylation of oxaloacetate in the absence of pyruvate could account for the difference in the amount of the two products formed during the overall reaction, it was postulated that the presence of pyruvate was necessary for hydrolysis to occur. Rate equations were derived describing the dependence of the initial velocity of the release of oxaloacetate in the overall reaction and the rate of the pyruvate:oxaloacetate exchange reaction, on pyruvate concentration. By assigning appropriate values to the various rate constants, theoretical curves were generated and fitted to the experimental data.     

Engineering microorganisms for improving polyhydroxyalkanoate biosynthesis

Manipulation bacterial cells for maximizing PHA synthesis.

     

Increasing rigor in NMR-based metabolomics through validated and open source tools

Opportunities and challenges ahead for NMR-based metabolomics.

     

The amino acid sequences of homologous hydroxyproline-containing myotoxins from the marine snail Conus geographus venom

Two homologous toxic peptides containing hydroxyproline from the venom of the marine snail Conus geographus have been sequenced.Geographutoxin I:

Geographutoxin II: Arg-Asp-Cys-Cys-Thr-Hyp-Hyp-Arg-Lys-Cys-Lys-Asp-Arg-Arg-Cys-Lys-Hyp-Met-Lys-Cys-Cys-Ala-NH₂These peptides inhibit the contractile response of directly stimulated mouse diaphragm.     

Stimuli-responsive polymeric materials for separation of biomolecules

Different stages in the SRP Virtuous Cycle for the development of temperature responsive polymers.

     

Role of iron and ethylenediaminetetraacetic acid in the bactericidal activity of a superoxide anion-generating system

In an earlier study, an enzymic superoxide anion-generating system consisting of acetaldehyde plus xanthine oxidase was found to be toxic to Staphylococcus aureus. Both superoxide anion (O

) and its dismutation product hydrogen peroxide (H₂O₂) were required and it was proposed that (O

) and H₂O₂ interact to form the more powerful bactericidal agent(s), hydroxyl radical (OH·) and/or singlet oxygen. Iron chelated by EDTA appears to be a heretofore unrecognized requirement for the xanthine oxidase bactericidal system. The evidence is as follows: (1) the addition of iron salts to the xanthine oxidase system increased bactericidal activity whereas the iron chelators diethylenetriaminepentaacetic acid (DTPA) and desferrioxamine were inhibitory; (2) dialysis of the EDTA-containing xanthine oxidase preparation abolished bactericidal activity which was restored on the addition of EDTA; (3) removal of trace amounts of iron by passage of salt solutions through a Chelex-100 column abolished bactericidal activity which was restored on the addition of iron.Iron and EDTA were most effective when present at 1:1 stoichiometry and they could not be replaced by a variety of other metals or chelators. The bactericidal activity of the acetaldehyde-xanthine oxidase-iron-EDTA system was inhibited by superoxide dismutase, catalase, and the OH · scavengers ethanol and mannitol, suggesting that the complex served as a catalyst of the reaction between (O

) and H₂O₂ to form OH· (Haber-Weiss reaction). Possible reasons for the relative catalytic specificity of iron-EDTA are considered.     

Next generation industrial biotechnology based on extremophilic bacteria

Next generation industrial biotechnology (NGIB) based on extremophilic bacteria grown under unsterile and continuous way in plastic transparent bioreactors.

     

Synthesis and subcellular distribution of heparan sulfate in the rat exocrine pancreas.

A kinetic study was conducted to investigate the properties of subsites S₁′ and S₂′ of α-chymotrypsin and subtilisin BPN′, which were deduced from model complexes with a pancreatic trypsin inhibitor and a hexapeptide substrate, respectively. For this purpose,

and

(AA, various amino acid residues) were synthesized. Since they were susceptible to cleavage at the positions shown by the arrows, we could examine the effect of P₁′ or P₂′ amino acid residue on hydrolysis [amino acid residues in peptide substrates and the corresponding subsites in enzymes are numbered according to the system of Schechter and Berger (1967)Biochem. Biophys. Res. Commun.27, 157–162]. The results agreed well with interactions of the leaving group with the corresponding subsites in both enzymes, which were deduced from the model complexes.