Home About us Contact
|
Home About us Contact | ||
|
|
||
R State (r + state)
Selected AbstractsThe X-ray structure determination of bovine carbonmonoxy hemoglobin at 2.1 Å resoultion and its relationship to the quaternary structures of other hemoglobin crystal formsPROTEIN SCIENCE, Issue 6 2001Martin K. Safo Abstract Crystallographic studies of the intermediate states between unliganded and fully liganded hemoglobin (Hb) have revealed a large range of subtle but functionally important structural differences. Only one T state has been reported, whereas three other quaternary states (the R state, B state, and R2 or Y state) for liganded Hb have been characterized; other studies have defined liganded Hbs that are intermediate between the T and R states. The high-salt crystal structure of bovine carbonmonoxy (CO bovine) Hb has been determined at a resolution of 2.1 Å and is described here. A detailed comparison with other crystallographically solved Hb forms (T, R, R2 or Y) shows that the quaternary structure of CO bovine Hb closely resembles R state Hb. However, our analysis of these structures has identified several important differences between CO bovine Hb and R state Hb. Compared with the R state structures, the ,-subunit N-terminal region has shifted closer to the central water cavity in CO bovine Hb. In addition, both the ,- and ,-subunits in CO bovine Hb have more constrained heme environments that appear to be intermediate between the T and R states. Moreover, the distal pocket of the ,-subunit heme in CO bovine Hb shows significantly closer interaction between the bound CO ligand and the Hb distal residues Val 63(E11) and His 63(E7). The constrained heme groups and the increased steric contact involving the CO ligand and the distal heme residues relative to human Hb may explain in part the low intrinsic oxygen affinity of bovine Hb. [source] Structure of relaxed-state human hemoglobin: insight into ligand uptake, transport and releaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2009Joy D. Jenkins Hemoglobin was one of the first protein structures to be determined by X-ray crystallography and served as a basis for the two-state MWC model for the mechanism of allosteric proteins. Since then, there has been an ongoing debate about whether Hb allostery involves the unliganded tense T state and the liganded relaxed R state or whether it involves the T state and an ensemble of liganded relaxed states. In fact, the former model is inconsistent with many functional observations, as well as the recent discoveries of several relaxed-state Hb structures such as RR2, R3 and R2. One school of thought has suggested the R2 state to be the physiologically relevant relaxed end state, with the R state mediating the T,R2 transition. X-ray studies have been performed on human carbonmonoxy Hb at a resolution of 2.8,Å. The ensuing liganded quaternary structure is different from previously reported liganded Hb structures. The distal ,-heme pocket is the largest when compared with other liganded Hb structures, partly owing to rotation of ,His63(E7) out of the distal pocket, creating a ligand channel to the solvent. The structure also shows unusually smaller ,- and ,-clefts. Results from this study taken in conjunction with previous findings suggest that multiple liganded Hb states with different quaternary structures may be involved in ligand uptake, stabilization, transport and release. [source] Structural flexibility, an essential component of the allosteric activation in Escherichia coli glucosamine-6-phosphate deaminaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2002E. Rudiño-Piñera A new crystallographic structure of the free active-site R conformer of the allosteric enzyme glucosamine-6-phosphate deaminase from Escherichia coli, coupled with previously reported structures of the T and R conformers, generates a detailed description of the heterotropic allosteric transition in which structural flexibility plays a central role. The T conformer's external zone [Horjales et al. (1999), Structure, 7, 527,536] presents higher B values than in the R conformers. The ligand-free enzyme (T conformer) undergoes an allosteric transition to the free active-site R conformer upon binding of the allosteric activator. This structure shows three alternate conformations of the mobile section of the active-site lid (residues 163,182), in comparison to the high B values for the unique conformation of the T conformer. One of these alternate R conformations corresponds to the active-site lid found when the substrate is bound. The disorder associated with the three alternate conformations can be related to the biological regulation of the Km of the enzyme for the reaction, which is metabolically required to maintain adequate concentrations of the activator, which holds the enzyme in its R state. Seven alternate conformations for the active-site lid and three for the C-terminus were refined for the T structure using isotropic B factors. Some of these conformers approach that of the R conformer in geometry. Furthermore, the direction of the atomic vibrations obtained with anisotropic B refinement supports the hypothesis of an oscillating rather than a tense T state. The concerted character of the allosteric transition is also analysed in view of the apparent dynamics of the conformers. [source] Avian haemoglobins and structural basis of high affinity for oxygen: structure of bar-headed goose aquomet haemoglobinACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2001Xiao-Zhou Liu Haemoglobin from the bar-headed goose (Anser indicus) has higher oxygen affinity than that from its lowland relatives such as greylag goose (A. anser). The crystal structure of bar-headed goose aquomet haemoglobin was determined at 2.3,Å resolution and compared with the structures of the goose oxy, human, horse and other avian haemoglobins and the sequences of other avian haemoglobins. Four amino-acid residues differ between greylag goose and bar-headed goose haemoglobins, among which Ala,119 and Asp,125 in bar-headed goose haemoglobin reduces the contacts between the ,1 and ,1 subunits compared with Pro and Glu, respectively, and therefore may increase the oxygen affinity by loosening the ,1,1 interface. Compared with human oxy haemoglobin, the relative orientation of two ,, dimers in the bar-headed goose aquomet and oxy Hbs are rotated by about 4°, indicating a unique quaternary structural difference from the typical R state. This new `RH' state is probably correlated with the higher oxygen affinity of bar-headed goose haemoglobin. [source] Preliminary neutron and X-ray crystallographic studies of equine cyanomethemoglobinACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 4 2010A. Y. Kovalevsky Room-temperature and 100,K X-ray and room-temperature neutron diffraction data have been measured from equine cyanomethemoglobin to 1.7,Å resolution using a home source, to 1.6,Å resolution on NE-CAT at the Advanced Photon Source and to 2.0,Å resolution on the PCS at Los Alamos Neutron Science Center, respectively. The cyanomethemoglobin is in the R state and preliminary room-temperature electron and neutron scattering density maps clearly show the protonation states of potential Bohr groups. Interestingly, a water molecule that is in the vicinity of the heme group and coordinated to the distal histidine appears to be expelled from this site in the low-temperature structure. [source] Reversible transition between active and dormant microbial states in soilFEMS MICROBIOLOGY ECOLOGY, Issue 2-3 2001John Stenström Abstract The rate of respiration obtained in the substrate-induced respiration (SIR) method can be divided into the respiration rate of growing (r) and non-growing (K) microorganisms. The fraction of r is generally small (5,20%) in soils with no recent addition of substrates, but can be 100% in soils with high substrate availability. This suggests that substrate availability determines the proportion of biomass between these groups, and implies that transitions between them can take place reversibly. These hypotheses were tested by adding three different amounts of glucose which induced first-order, zero-order, and growth-associated respiration kinetics to three soils at four pre-incubation times (4, 12, 27, and 46 days) before the SIR measurement. An abiotic flush of CO2 in the SIR measurement was detected and corrected for before data analysis. Accumulated CO2 -C over 4 days after glucose addition, corrected for the respiration in unamended controls, corresponded to 41,50% mineralization of the glucose-C, and the relative amount mineralized by each soil was independent of the glucose amount added. The high glucose concentration gave an increased SIR, which reverted to the initial value within 27,46 days. In a specific sample, the maximum respiration rate induced during the pre-incubation, and the amount of organisms transformed from the K to the r state, as quantified in respiration rate units in the SIR measurement, were identical to each other, and these parameters were also highly correlated to the initial glucose concentration. The K,r transition was very fast, probably concurrent with the instantaneous increase in the respiration rate obtained by the glucose amendment. Thereafter, a slow first-order back-transition from the r to the K state ensued, with half-lives of 12, 23, and 70 days for the three soils. The results suggest the existence of community-level controls by which growth within or of the whole biomass is inhibited until it has been completely transformed into the r state. The data also suggest that the microbial specific activity is not related to the availability of exogenous substrate in a continuous fashion, rather it responds as a sharp transition between dormant and fully active. Furthermore, the inherent physiological state of the microbial biomass is strongly related to its history. It is proposed that the normal dynamics of the soil microbial biomass is an oscillation between active and dormant physiological states, while significant growth occurs only at substantial substrate amendment. [source] | ||||||||||