Single Conformational State Research Articles

Structure of the N-terminal fragment of topoisomerase V reveals a new family of topoisomerases

Topoisomerases are involved in controlling and maintaining the topology of DNA and are present in all kingdoms of life. Unlike all other types of topoisomerases, similar type IB enzymes have only been identified in bacteria and eukarya. The only putative type IB topoisomerase in archaea is represented by Methanopyrus kandleri topoisomerase V. Despite several common functional characteristics, topoisomerase V shows no sequence similarity to other members of the same type. The structure of the 61 kDa N-terminal fragment of topoisomerase V reveals no structural similarity to other topoisomerases. Furthermore, the structure of the active site region is different, suggesting no conservation in the cleavage and religation mechanism. Additionally, the active site is buried, indicating the need of a conformational change for activity. The presence of a topoisomerase in archaea with a unique structure suggests the evolution of a separate mechanism to alter DNA.

Towards the structure of the BchI hexameric complex of magnesium chelatase

The insertion of Mg into protoporphyrin IX is catalyzed by the enzyme magnesium chelatase and represents the first committed step in the chlorophyll and bacteriochlorophyll biosynthetic pathways. Magnesium chelatase, in organisms that synthesize bacteriochlorophyll, consists of three subunits, known as BchI, BchD and BchH. The structure of the monomeric BchI has been determined by X-Ray crystallography and it belongs to the chaperone-like, ATPase associated with a variety of cellular activities, (AAA) family of ATPases. Examination by electron microscopy of BchI solutions in the presence of ATP demonstrated that BchI, like other AAA proteins, forms oligomeric ring structures, [1]. The ATP hydrolysis is proposed to trigger major conformational changes in the hexamer, as has been shown for other AAA modules, [2]. Thus, it is crucial to fixate the complex in one single conformational state using non-hydrolysable substrates to create a homogenous environment. Needle shaped protein crystals have been obtained in different conditions. Ongoing optimization of crystallization conditions will hopefully give single crystals suitable for X-ray diffraction.

Structural Heterogeneity in DNA: Temperature Dependence of 2‐Aminopurine Fluorescence in Dinucleotides

The fluorescent base analogue 2-aminopurine is a sensitive probe for local dynamics of DNA. Its fluorescence is quenched by interaction with the neighboring bases, but the underlying mechanisms are still under investigation. We studied 2-aminopurine fluorescence in dinucleotides with each of the natural bases. Consistently, two of the four fluorescence-decay components depend strongly on temperature. Our results indicate that these components are due to the excited-state dynamics of a single conformational state. We propose a variation of the gating model in which transient unstacking occurs in the excited state.

Comparison of cell‐based and cell‐free protocols for producing target proteins from theArabidopsis thalianagenome for structural studies

We describe a comparative study of protein production from 96 Arabidopsis thaliana open reading frames (ORFs) by cell-based and cell-free protocols. Each target was carried through four pipeline protocols used by the Center for Eukaryotic Structural Genomics (CESG), one for the production of unlabeled protein to be used in crystallization trials and three for the production of 15N-labeled proteins to be analyzed by 1H-15N NMR correlation spectroscopy. Two of the protocols involved Escherichia coli cell-based and two involved wheat germ cell-free technology. The progress of each target through each of the protocols was followed with all failures and successes noted. Failures were of the following types: ORF not cloned, protein not expressed, low protein yield, no cleavage of fusion protein, insoluble protein, protein not purified, NMR sample too dilute. Those targets that reached the goal of analysis by 1H-15N NMR correlation spectroscopy were scored as HSQC+ (protein folded and suitable for NMR structural analysis), HSQC+/- (protein partially disordered or not in a single stable conformational state), HSQC- (protein unfolded, misfolded, or aggregated and thus unsuitable for NMR structural analysis). Targets were also scored as X- for failing to crystallize and X+ for successful crystallization. The results constitute a rich database for understanding differences between targets and protocols. In general, the wheat germ cell-free platform offers the advantage of greater genome coverage for NMR-based structural proteomics whereas the E. coli platform when successful yields more protein, as currently needed for crystallization trials for X-ray structure determination.

Structural studies of wheat flour glutenin polymers by CD spectroscopy.

A dissolution procedure of unreduced glutenin polymers of three wheat flour varieties (WRU 6981, Alisei 1, and Alisei 2) by sonication in the presence of SDS (sodium dodecyl sulphate), after the elimination of albumins, globulins, and gliadins, was achieved, and the molecular weight distribution of glutenin polymers obtained by this method was measured by matrix assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry. A structural study by CD spectroscopy at different temperatures of WRU 6981 glutenin polymer and of 1Ax1 high-M(r) (relative molecular mass) glutenin subunit, which is the only high-M(r) subunit contained in WRU 6981 flour, was undertaken to understand if the information obtained from the single subunit were applicable to the total polymer. CD spectroscopy also has been employed to study the glutenin polymers obtained by Alisei 1 and Alisei 2 wheat flours; Alisei 1 biotype contained 1Bx7 and 1Dx2+1Dy12 high-M(r) subunits, whereas the Alisei 2 biotype contained only 1Bx7 and 1Dy12 subunits. A conformational study was undertaken by CD spectroscopy at different temperatures and in the presence of some chemical denaturant agents, such as urea and sodium dodecyl sulphate, in order to obtain information about their intrinsic stability and to verify if the 1Dx2 subunit presence determined a different structural behavior between Alisei 1 and Alisei 2 polymers. MALDI-TOF mass spectrometric experiments showed that the glutenin polymers molecular weights were in the mass range of 500000-5000000. CD spectra indicated that a single conformational state did not predominate in the temperature range studied but equilibrium between two distinct conformational states existed; moreover, all the changes induced by urea and by SDS followed a multistep transition process.

Matrix-isolation and solid state low temperature FT-IR study of 2,3-butanedione (diacetyl)

2,3-Butanedione (diacetyl) was studied by matrix-isolation and low temperature solid state FT-IR spectroscopy, supported by molecular orbital calculations undertaken at the DFT(B3LYP) and MP2 levels of theory with the 6-311++G(d,p) basis set. Both in the crystalline phase and in the matrices, the compound exists in the C 2h symmetry trans conformation (OC–CO dihedral angle of 180°). This form corresponds to the single conformational state predicted by the theoretical calculations for the compound in vacuum. However, in the low temperature amorphous state, obtained by fast deposition of the vapour of the compound onto a suitable cold (9 K) substrate, as well as in the liquid and gaseous phases, spectroscopic features are observed that can only be explained by assuming that conformations without an inversion centre ( C 2 symmetry) do also contribute to the spectra. These results are in agreement with the experimental evidence that diacetyl has a permanent dipole moment (ca.1 Debye) in the vapour phase at room temperature and are here explained taking into consideration the influence of the low frequency large amplitude torsional vibration around the central C–C bond on the molecular properties.

Identification of conformational substates involved in nitric oxide binding to ferric and ferrous myoglobin through difference Fourier transform infrared spectroscopy (FTIR).

Hemeproteins play an important role in the signaling processes mediated by nitric oxide (NO). For example, the production of NO by nitric oxide synthase, the activation of guanylate cyclase by binding NO, and the scavenging of NO by hemoglobin, myoglobin, and cytochrome c oxidase all occur through unique mechanisms of interaction between NO and hemeproteins. Unlike carbon monoxide (CO) and oxygen (O2), which have been studied extensively, the reactions of NO with ferric and ferrous hemeproteins are not as well characterized. In this work, NO binding to myoglobin is studied using cryogenic optical spectroscopy and Fourier transform infrared spectroscopy (FTIR) in order to characterize the ligand-bound and photoproduct states involved in the interaction of NO with the heme iron and the distal pocket of the protein. For ferrous nitrosyl myoglobin (MbIINO), optical spectroscopy is used to show that the ligand-bound state can be converted to >95% stable photoproduct below 10 K. The Soret peak of the photoproduct is red-shifted by 4 nm relative to deoxy-myoglobin (Mb), similar to previous results for carbonmonoxy- (MbCO) and oxy-myoglobin (MbO2) (Miller et al., 1996). MbIINO completely rebinds by 35 K, indicating that the rebinding barrier for NO is lower than MbCO, consistent with room temperature picosecond kinetic measurements. For ferric nitrosyl myoglobin (MbIIINO), we find that the photoproduct yield at cryogenic temperatures is less than unity and dependent on the distal pocket residue. Native MbIIINO has a lower photoproduct yield than the mutant, MbIII(H64L)NO, where the distal histidine is replaced by leucine. The rebinding rates for the native and mutant species are similar to each other and to MbIINO. By using FTIR difference spectroscopy (photolyzed/unphotolyzed) of isotopically labeled ferrous nitrosyl myoglobin (MbIINO), the NO stretching frequencies in both the ligand-bound states and photoproduct states are determined. Two ligand-bound conformational states (1607 and 1613 cm-1) and two photoproduct conformational states (1852 and 1857 cm-1) are observed for MbIINO. This is the first direct observation of photolyzed NO in the distal pocket of myoglobin. The ligand-bound frequencies are consistent with a bent MbIINO moiety, where the unpaired pi*(NO) electron remains localized on NO, causing nu(N-O) to be approximately 300 cm-1 lower than MbIIINO. Similar to MbO2, we suggest that Nepsilon of the distal histidine is protonated, forming a hydrogen bond to the NO ligand. For native MbIIINO, a single ligand-bound conformational state with respect to nu(N-O) is observed at 1927 cm-1. This frequency decreases to 1904 cm-1 for the mutant, MbIII(H64L)NO, contrary to the increase of the carbon monoxide (CO) stretching frequency in the isoelectronic MbII(H64L)CO mutant versus native MbCO. For linear MbIIINO, we suggest that backbonding from the unpaired pi*(NO) electron to iron results in an increased positive charge on the NO ligand, Fe(delta-)-NO(delta+). This can be facilitated by tautomerism of the distal histidine, leaving Nepsilon of the imidazole ring unprotonated and able to accept positive charge from the Fe(delta-)-NO(delta+) moiety, resulting in a higher bond order (and a 23 cm-1 shift to higher frequency) for native MbIIINO versus MbIII(H64L)NO, where this interaction is absent. These different interactions between the distal histidine and the ferrous versus ferric species illustrate potential ways the protein can stabilize the bound ligand and demonstrate the versatile nature by which NO can bind to hemeproteins.

3H-n.m.r. studies of multiple conformations and dynamic processes in complexes of folate and methotrexate with Lactobacillus casei dihydrofolate reductase

[7,3',5'-3H3]- and [7,9-3H3]-folic acid and [7,3',5'-3H3]methotrexate (MTX) have been prepared and 3H-n.m.r. spectra obtained for their complexes with Lactobacillus casei dihydrofolate reductase (DHFR). The 3H results confirm the presence of three pH-dependent different conformational forms in the complex DHFR.NADP+.folate. The folate benzoyl ring could be shown to be in essentially the same environment in the different forms, with the major differences being associated with the pterin ring. The appearance of a single resonance for the 3',5'-tritons showed that the benzoyl ring is flipping rapidly in all three forms. In contrast, the MTX complex was shown to exist as a single conformational state with the benzoyl ring flipping rate being too low to give a single averaged signal for the 3',5'-nuclei over the temperature range 283-313 K.

L-659,989: a useful probe in the detection of multiple conformational states of PAF receptors.

L-659,989 is a potent, specific and competitive platelet-activating factor (PAF) receptor antagonist. The 2,5-tritium labeled L-659,989, similar to [3H]PAF, specifically binds to rabbit platelet membranes with an equilibrium dissociation constant (KD) of 1.60 (+/- 0.20) nM in 10 mM MgCl2. However, guanosine 5'-triphosphate (GTP) and several cations affect the specific binding of [3H]PAF and of [3H]L-659,989 to rabbit platelet membranes in different ways. K+, Mg2+, Ca2+ and Mn2+ potentiate the specific binding of both ligands. Na+ and Li+ inhibit the specific [3H]PAF binding, but enhance the binding of [3H]L-659,989; GTP reduces the [3H]PAF binding but has no effect on the binding of [3H]-L-659,989. Ni2+ inhibits the [3H]L-659-989 binding, but has no effect on the binding of [3H]PAF. In the presence of 150 mM NaCl, [3H]L-659,989 exhibits identical KD and detectable binding sites (Bmax) values as those in the presence of 10 mM MgCl2, while KD And Bmax values of [3H]PAF are dramatically reduced in the presence of 150 mM NaCl compared to those in 10 mM MgCl2. These results suggest the existence of multiple conformational states of the PAF specific receptor and that PAF and L-659,989 bind differently to those states. In the presence of 150 mM NaCl and 1 mM GTP, receptors appear to exist in a single conformational state with an equilibrium dissociation constant (KB) of 0.93 microM for PAF as derived from the Schild plot. In isolated rabbit platelets pretreated with 10 microM ETH 227, a Na(+)-specific ionophore, the detectable [3H]PAF binding sites drop from 260 to 100 binding sites per platelet, but the binding sites for [3H]L-659,989 remain roughly the same. The Na+ binding sites which modulate the conformation of PAF receptors are therefore protected from extracellular Na+ until ionophore is added, and are probably located on the cytoplasmic side of the plasma membrane.

Atomic force microscopy of biological samples at low temperature

The atomic force microscope (AFM) has been successful imaging rigid samples with atomic resolution, but this resolution has not been matched on soft biological samples at room temperature. On many biological samples even tracking forces as small as 10−9 N distort the sample during a scan.At low temperatures proteins freeze into a single conformational state and become much more rigid. In this paper we demonstrate that it should be feasible to get atomic resolution on frozen biological samples with a low-temperature AFM. We also show some preliminary low-temperature AFM images of one biological sample, purple membrane.

Effects of thermodynamic nonideality on the kinetics of ester hydrolysis by α-chymotrypsin: A model system with preexistence of the isomerization equilibrium

The effects of a small inert solute, sucrose, on the kinetics of hydrolysis of N-acetyl-tryptophan ethyl ester by bovine α-chymotrypsin have been investigated. In studies at pH 7 and 20 °C the presence of 0.5 m sucrose in assay mixtures caused no discernible change in kinetic parameters, a result consistent with existence of the enzyme in a single conformational state under those conditions. However, at pH 3.5 and 50 °C, conditions under which the enzyme comprises an equilibrium mixture of compact and expanded isomeric states, inclusion of the inert solute led to a considerable decrease in Michaelis constant (0.84 to 0.61 m m) but no significant change in maximal velocity. These results were shown to be amenable to quantitative interpretation in terms of thermodynamic nonideality effects on catalysis by an enzyme undergoing reversible isomerization in the absence of substrate. For that analysis, which required experimental estimates of the equilibrium constant for preexisting isomerization of enzyme and the activity coefficient of substrate, the magnitude of the former (0.3) was obtained by difference spectroscopy: liquid-liquid partition studies with bromobenzene as organic phase were used to determine the effect of sucrose on the activity coefficient of N-acetyltryptophan ethyl ester. Such agreement between experimental kinetic findings and theoretical predictions based on considerations of excluded volume points to the possible use of the space-filling effects of small solutes for delineating the gross extent of conformational changes associated with reversible isomerization of proteins, and hence to the potential of thermodynamic nonideality as a probe for studying protein denaturation mechanisms as well as substrate-mediated changes associated with enzyme reaction mechanisms.

Comparison of the substrate conformations in the active sites of papain, chymopapain, ficin and bromelain by resonance Raman spectroscopy

The resonance Raman spectra of several enzyme-substrate intermediates of papain, chymopapain, ficin and bromelain are reported. The intermediates are dithioacyl enzymes formed during the catalyzed hydrolysis of N -acylglycine thionoester substrates. Interpretation of the resonance Raman spectra allows us to compare, for the first time, the substrate geometries in a series of functioning intermediates from different enzymes. The substrates assume essentially identical conformations for papain, chymopapain and ficin and a similar, but not identical, conformation in the active site of bromelain. Each dithioacyl enzyme population appears to be made up of a single homogeneous conformational state. This state has been characterised in earlier studies of dithioacyl papains. It is designated as conformer B and is characterized by an attractive contact between the substrate's glycinic N atom and the active site cysteine S atom. It is now apparent that conformer B is of general significance in the mechanism of cysteine proteases.

Proton magnetic relaxation of aspartate transcarbamylase - succinate complexes.

Nuclear magnetic relaxation methods were used to investigate the interaction of the inhibitor succinate with aspartate transcarbamylase from Escherichia coli. Over the pH range 7 to 9, the dissociation constant for succinate remains less than the inhibitor concentration used for most of this work (0.05 M). As a result, the enzyme predominantly exists in a single "gross" conformational state. Succinate binding to this enzyme state (generally known as the R form) parallels the behavior seen previously with the isolated catalytic subunit (Beard, C. B., and Schmidt, P.G. (1973) Biochemistry 12, 2255-2264). The pH and temperature dependence of succinate proton relaxation rates, 1/T2 - 1/T1, in the presence of carbamyl phosphate, is interpreted in terms of a binding mechanism involving three forms of the enzyme, differing by their states of protonation. The least protonated form of the enzyme does not interact with succinate, the singly protonated species binds succinate to form a rapidly dissociating complex, and the doubly protonated species undergoes a conformational isomerization upon succinate binding, yielding a slow exchange complex. Relaxation data provide sufficient information to determine pKa values of 7.2 and 8.9 for two ionizing groups, as well as the dissociation constant for succinate in the fast exchange complex, Kd =1.6 X 10(-2) M. Rate constants for the forward and reverse steps of the isomerization, 1.3 X 10(3) s-1 and 33 s-1, respectively, indicate a significantly slower reverse rate from that obtained in the earlier NMR study of the isolated catalytic subunit. In experiments where the succinate concentration was varied, the relaxation rates showed sigmoidal binding of that ligand to the fast exchange complex above pH 9.1, (a) indicating cooperative binding of succinate, and (b) suggesting that above pH 9.1, the system cannot be characterized by a single dissociation constant, ionization constant, or relaxation effect. CTP and ATP were tested for their ability to affect succinate binding to the fast exchange complex. Heterotropic interactions were observed for CTP but not for ATP. Addition of low concentrations of the transition state analog N-(phosphonacetyl)-L-aspartate to the enzyme-carbamyl phosphate-succinate complex sharply decreased the relaxation rate, indicating that the measurements are sensitive only to succinate bound specifically to the active site.