A new approach to the characterization of the B and A forms of DNA by I.R. spectroscopy

The RNA conformational changes of B, A and C forms are reflected in the infrared absorption spectra in the region of 800 cm^?1 to 900 cm^?1 and allow one to investigate unoriented samples. The transition to the A form is characterized by the appearence of bands at about 870 cm^?1 and at 813 cm^?1 whereas the B and the C forms exhibit a band at 837 cm^?1, these bands undoubtedly arise from phosphate diester stretching vibrations and yield information about backbone conformation. The presence of these infrared bands provides a criterion for testing the simultaneous presence of two coexisting forms of DNA. It represents a useful method for structural studies of nucleic acid complexes such as protein-DNA for which it is difficult to obtain orientation.     

Conformational changes in the archaerhodopsin-3 proton pump: detection of conserved strongly hydrogen bonded water networks

Archaerhodopsin-3 (AR3) is a light-driven proton pump from Halorubrum sodomense, but little is known about its photocycle. Recent interest has focused on AR3 because of its ability to serve both as a high-performance, genetically-targetable optical silencer of neuronal activity and as a membrane voltage sensor. We examined light-activated structural changes of the protein, retinal chromophore, and internal water molecules during the photocycle of AR3. Low-temperature and rapid-scan time-resolved FTIR-difference spectroscopy revealed that conformational changes during formation of the K, M, and N photocycle intermediates are similar, although not identical, to bacteriorhodopsin (BR). Positive/negative bands in the region above 3,600 cm^− 1, which have previously been assigned to structural changes of weakly hydrogen bonded internal water molecules, were substantially different between AR3 and BR. This included the absence of positive bands recently associated with a chain of proton transporting water molecules in the cytoplasmic channel and a weakly hydrogen bonded water (W401), which is part of a hydrogen-bonded pentagonal cluster located near the retinal Schiff base. However, many of the broad IR continuum absorption changes below 3,000 cm^− 1 assigned to networks of water molecules involved in proton transport through cytoplasmic and extracellular portions in BR were very similar in AR3. This work and subsequent studies comparing BR and AR3 structural changes will help identify conserved elements in BR-like proton pumps as well as bioengineer AR3 to optimize neural silencing and voltage sensing.     

Molecular structure of malate synthase and structural changes upon ligand binding to the enzyme

Malate synthase has a molecular weight of about 170 000 as shown by ultracentrifugation, sucrose gradient centrifugation, and thin layer gel-chromatography. High dilution, extremes of pH, succinylation, and treatment with sodium dodecylsulfate suggest the enzyme to be a tetramer. The CD spectrum is typical for a globular protein with moderate helical content (～30 %), and shows anomalous Cotton effects at 250–290 nm. Binding of substrates (acetyl-CoA, glyoxylate) or the substrate analog pyruvate causes slight conformational changes which are reflected in alterations of the CD bands in the range of aromatic absorption; binding of Mg²⁺ causes no structural effects, suggesting the metal ion to be involved in enzymatic catalysis rather than structural alterations.     

Molecular modeling study for conformational changes of Sirtuin 2 due to substrate and inhibitor binding

Sirtuin is a member of NAD⁺-dependent deacetylase family. The structural details of Sirtuin 2 (SIRT2) complex will be very useful to discover the drug which might have beneficial effects on various diseases like cancer, diabetes, etc. Unfortunately, SIRT2 complex structure is not available yet, hence molecular docking was carried out to dock the substrate (NAD⁺ and acetylated lysine) and inhibitor (sirtinol) in the NAD⁺ binding site. The suitable binding orientation of substrate and inhibitor in the SIRT2 active site was selected and subjected to 5?ns molecular dynamics simulations to adjust the binding orientation of inhibitor and substrate as well as to identify the conformational changes in the active site. The result provides an insight about 3D SIRT2 structural details as well as the importance of F96 in deacetylation function. In addition, our simulations revealed the displacement of F96 upon substrate and inhibitor binding, inducing an extended conformation of loop3 and changing its interactions with the rest of SIRT2. We believe that our study could be helpful to gain a structural insight of SIRT2 and to design the receptor-based inhibitors.     

The effects of stretch activation on ionic selectivity of the TREK-2 K2P K+ channel

The TREK-2 (KCNK10) K2P potassium channel can be regulated by variety of polymodal stimuli including pressure. In a recent study, we demonstrated that this mechanosensitive K⁺ channel responds to changes in membrane tension by undergoing a major structural change from its ‘down’ state to the more expanded ‘up’ state conformation. These changes are mostly restricted to the lower part of the protein within the bilayer, but are allosterically coupled to the primary gating mechanism located within the selectivity filter. However, any such structural changes within the filter also have the potential to alter ionic selectivity and there are reports that some K2Ps, including TREK channels, exhibit a dynamic ionic selectivity. In this addendum to our previous study we have therefore examined whether the selectivity of TREK-2 is altered by stretch activation. Our results reveal that the filter remains stable and highly selective for K⁺ over Na⁺ during stretch activation, and that permeability to a range of other cations (Rb⁺, Cs⁺ and NH₄⁺) also does not change. The asymmetric structural changes that occur during stretch activation therefore allow the channel to respond to changes in membrane tension without a loss of K⁺ selectivity.     

Localization of light-induced structural changes in bacterial photosynthetic reaction centers

Light-induced structural changes in photosynthetic reaction centers from Rhodobacter sphaeroides were investigated using two approaches. Cu²⁺ was used as a paramagnetic structural probe. The EPR spectrum of Cu²⁺ incorporated into the metal-depleted reaction centers was affected by 1,10-phenanthroline, an electron transfer inhibitor substituting Q_B, which suggests a localization of Cu²⁺ in a vicinity of the Q _B ^– site. However, the spectrum was not influenced by low temperature (77 K) illumination of the sample which suggests that the copper ion position is not exactly the same as that of the iron ion. Freezing the reaction centers under illumination in the presence of potassium ferricyanide and 1,10-phenanthroline caused a change in the shape of the Cu²⁺ EPR spectrum in comparison to that of a sample frozen in darkness. These data indicate a change of the Cu²⁺ ligand symmetry owing to light-induced structural changes which are probably located near the acceptor side of the reaction center. Partial trypsinolysis of reaction centers was also used to locate the structural changes. Trypsin treatment in the dark and under illumination resulted in different peptide patterns as detected by gel electrophoresis and reverse-phase high-performance liquid chromatography. Partial amino-acid sequence analysis of a number of peptides, characteristic of either light- or dark-treated reaction centers, showed that they originated from the acceptor sides of the H and M subunits. The occurrence of light-induced structural differences in the H-subunit is consistent with the suggestion that it may be involved in regulating electron transfer in this part of the reaction center.     

Structural Changes in the N and N′ States of the Bacteriorhodopsin Photocycle

The bacteriorhodopsin transport cycle includes protonation of the retinal Schiff base by Asp⁹⁶ (M→N reaction) and reprotonation of Asp⁹⁶ from the cytoplasmic surface (N→N′ reaction). We measured distance changes between pairs of spin-labeled structural elements of interest, and in general observed larger overall structural changes in the N state compared with the N′ state. The distance between the C-D loop and E-F interhelical loops in A103R1/M163R1 increased ∼6 Å in the N state and ∼3 Å in the N′ state. The opposite trend of distance changes in V101R1/A168R1 and L100R1/T170R1 supports counterclockwise rotation of helix F in the N but not the N′ state. Small distance increases were observed in S169R1/S226R1, but little change was seen in G106R1/G155R1. Taking earlier published EPR data into account, we suggest that structural changes of the E-F loop occur first, and then helices F and G begin to move together in the late M state. These motions then reach their maximum amplitude in the N state, evidently to facilitate the release of a proton from Asp⁹⁶ and the formation of a proton-conduction pathway from Asp⁹⁶ to the Schiff base. The structural changes reverse their directions and decay in the N′ state.     

Structural and functional changes in the malpighian tubules of Carausius morosus during dehydration and starvation

Summary Carausius morosus starved and deprived of water lose about 30% of their body weight in 4 days, mainly due to water loss. Isolated inferior tubules from starved dehydrated insects secrete urine at 0.041 nl·mm^–1·min^–1 compared with 0.118 nl·mm^–1·min^–1 in those from fed hydrated insects. This difference is due partly to the level of a diuretic (and perhaps also an antidiuretic) hormone in the haemolymph acting directly on the urine-secreting mechanism and partly to changes in the intrinsic capacity of the tubule cells for urine secretion. This latter change is accompanied by structural changes in the tubules. During starvation and dehydration the lumen becomes packed with white granules, the height of the type 1 cells is reduced, their basal infoldings and brush border become shorter and their mitochondrial volume is reduced.     

A Raman scattering study of the interactions of DNA with its water of hydration

Raman spectroscopy is used to probe the nature of the hydrogen bonds which hold the water of hydration to DNA. The ～ 3450?cm^?1 molecular O–H stretching mode shows that the first six water molecules per base pair of the primary hydration shell are very strongly bound to the DNA. The observed shift in the peak position of this mode permits a determination of the length of the hydrogen bonds for these water molecules. These hydrogen bonds appear to be about 0.3?Å shorter than the hydrogen bonds in bulk water. The linewidth of this mode shows no significant changes above water contents of about 15 water molecules per base pair. This technique of using a vibrational spectroscopy to obtain structural information about the hydration shells of DNA could be used to study the hydration shells of other biomolecules.     

Spectroscopic Determination of Lysozyme Conformational Changes in the Presence of Trehalose and Guanidine

The bioprotective action of the disaccharide trehalose has been studied against the well-known denaturating agent, guanidine hydrochloride. The results indicated a direct influence of trehalose on both enzymatic activity and conformational changes of lysozyme, as shown by the decrease of the inactivation rate constant of about 1.48-fold and the loss of α-helix structure of lysozyme. In addition, ESI–MS hydrogen–deuterium (H/D) exchange experiments allowed us to correlate the structural and dynamic features of the protein in the presence of the two additives, highlighting as trehalose remarkably influenced this exchange by decreasing local protein environment changes and solvent accessibility to the amide peptide backbone, as further evidenced by circular dichroism and ¹H NMR measurements.     

Structural and Kinetic Effects of PAK3 Phosphorylation Mimic of cTnI(S151E) on the cTnC-cTnI Interaction in the Cardiac Thin Filament

Residue Ser151 of cardiac troponin I (cTnI) is known to be phosphorylated by p21-activated kinase 3 (PAK3). It has been found that PAK3-mediated phosphorylation of cTnI induces an increase in the sensitivity of myofilament to Ca²⁺, but the detailed mechanism is unknown. We investigated how the structural and kinetic effects mediated by pseudo-phosphorylation of cTnI (S151E) modulates Ca²⁺-induced activation of cardiac thin filaments. Using steady-state, time-resolved Förster resonance energy transfer (FRET) and stopped-flow kinetic measurements, we monitored Ca²⁺-induced changes in cTnI-cTnC interactions. Measurements were done using reconstituted thin filaments, which contained the pseudo-phosphorylated cTnI(S151E). We hypothesized that the thin filament regulation is modulated by altered cTnC-cTnI interactions due to charge modification caused by the phosphorylation of Ser151 in cTnI. Our results showed that the pseudo-phosphorylation of cTnI (S151E) sensitizes structural changes to Ca²⁺ by shortening the intersite distances between cTnC and cTnI. Furthermore, kinetic rates of Ca²⁺ dissociation-induced structural change in the regulatory region of cTnI were reduced significantly by cTnI (S151E). The aforementioned effects of pseudo-phosphorylation of cTnI were similar to those of strong crossbridges on structural changes in cTnI. Our results provide novel information on how cardiac thin filament regulation is modulated by PAK3 phosphorylation of cTnI.     

Infrared spectroscopic study of the structural and functional properties of the Na/H antiporter MjNhaP1 from Methanococcus jannaschii

In this study, structural, functional, and mechanistic properties of the Na⁺/H⁺ antiporter MjNhaP1 from Methanococcus jannaschii were analyzed by infrared spectroscopic techniques. Na⁺/H⁺ antiporters are generally responsible for the regulation of cytoplasmic pH and Na⁺ concentration. MjNhaP1 is active in the pH range between pH 6 and pH 6.5; below and above it is inactive.The secondary structure analysis on the basis of ATR-IR spectra provides the first insights into the structural changes between inactive (pH 8) and active (pH 6) state of MjNhaP1. It results in decreased ordered structural elements with increasing the pH-value i.e. with inactivation of the protein. Analysis of temperature-dependent FTIR spectra indicates that MjNhaP1 in the active state exhibits a much higher unfolding temperature in the spectral region assigned to α-helical segments. In contrast, the temperature-induced structural changes for β-sheet structure are similar for inactive and active state. Consequently, this structure element is not the part of the activation region of the protein. The surface accessibility of the protein was analyzed by following the extent of H/D exchange. Due to higher content of unordered structural elements a higher accessibility for amide protons is observed for the inactive as compared to the active state of MjNhaP1. Altogether, the results present the active state of MjNhaP1 as the state with ordered structural elements which exhibit high thermal stability and increased hydrophobicity.     

Structural and functional changes of the articular surface in a post-traumatic model of early osteoarthritis measured by atomic force microscopy

The functional integrity of the articulating cartilage surface is a critical determinant of joint health. Although a variety of techniques exist to characterize the structural changes in the tissue with osteoarthritis (OA), some with extremely high resolution, most lack the ability to detect and monitor the functional changes that accompany the structural deterioration of this essential bearing surface. Atomic force microscopy (AFM) enables the acquisition of both structural and mechanical properties of the articular cartilage surface, with up to nanoscale resolution, making it particularly useful for evaluating the functional behavior of the macromolecular network forming the cartilage surface, which disintegrates in OA.In the present study, AFM was applied to the articular cartilage surfaces from six pairs of canine knee joints with post-traumatic OA. Microstructure (RMS roughness) and micromechanics (dynamic indentation modulus, E^?) of medial femoral condyle cartilages were compared between contralateral controls and cruciate-transected knee joints, which develop early signs of OA by three months after surgery.Results reveal a significant increase in RMS roughness and a significant four-fold decrease in E^? in cartilages from cruciate-transected joints versus contralateral controls. Compared to previous reports of changes in bulk mechanics, AFM was considerably more sensitive at detecting early cartilage changes due to cruciate-deficiency. The use of AFM in this study provides important new information on early changes in the natural history of OA because of its ability to sensitively detect and measure local structural and functional changes of the articular cartilage surface, the presumptive site of osteoarthritic initiation.     

Atomic model of an infectious rotavirus particle

Non‐enveloped viruses of different types have evolved distinct mechanisms for penetrating a cellular membrane during infection. Rotavirus penetration appears to occur by a process resembling enveloped‐virus fusion: membrane distortion linked to conformational changes in a viral protein. Evidence for such a mechanism comes from crystallographic analyses of fragments of VP4, the rotavirus‐penetration protein, and infectivity analyses of structure‐based VP4 mutants. We describe here the structure of an infectious rotavirus particle determined by electron cryomicroscopy (cryoEM) and single‐particle analysis at about 4.3 Å resolution. The cryoEM image reconstruction permits a nearly complete trace of the VP4 polypeptide chain, including the positions of most side chains. It shows how the two subfragments of VP4 (VP8^* and VP5^*) retain their association after proteolytic cleavage, reveals multiple structural roles for the β‐barrel domain of VP5^*, and specifies interactions of VP4 with other capsid proteins. The virion model allows us to integrate structural and functional information into a coherent mechanism for rotavirus entry.     

Effects of endogenous and exogenous processes on aboveground biomass stocks and dynamics in Andean forests

Tropical forests are paramount in regulating the global carbon cycle due to the storage of large amounts of carbon in their biomass. Using repeat censuses of permanent plots located at 15 sites in the Andes Mountains of northwest Colombia, we evaluate: (1) the relationship between aboveground biomass (AGB) stocks, AGB dynamics (mortality, productivity, and net change), and changes in temperature across a ca. 3000-m elevational gradient (≈?16.1 °C); (2) how AGB mortality and AGB productivity interact to determine net AGB change; and (3) the extent to which either fine-grain (0.04-ha) or coarse-grain (1-ha) processes determine the AGB dynamics of these forests. We did not find a significant relationship between elevation/temperature and biomass stocks. The net AGB sequestered each year by these forests (2.21?±?0.51 Mg ha^?1 year^?1), equivalent to approximately 1.09% of initial AGB, was primarily determined by tree growth. Both forest structural properties and global warming influenced AGB mortality and net change. AGB productivity increases with greater inequality of tree sizes, a pattern characteristic of forest patches recovering from disturbances. Overall, we find that global warming is triggering directional changes in species composition by thermophilization via increased tree mortality of species in the lower portions of their thermal ranges and that the inclusion of small-scale forest structural changes can effectively account for endogenous processes such as changes in forest structure. The inclusion of fine-grain processes in assessments of AGB dynamics could provide additional insights about the effects that ongoing climate change has on the functioning of tropical montane forests.     

Drug–DNA Interaction Studies of Acridone-Based Derivatives

N¹⁰-alkylated 2-bromoacridones are a novel series of potent antitumor compounds. DNA binding studies of these compounds were carried out using spectrophotometric titrations, Circular dichroism (CD) measurements using Calf Thymus DNA (CT DNA). The binding constants were identified at a range of K = 0.3 to 3.9 × 10⁵ M^?1 and the percentage of hypochromism from the spectral titrations at 28–54%. This study has identified a compound 9 with the good binding affinity of K = 0.39768 × 10⁵ M^?1 with CT DNA. Molecular dynamics (MD) simulations have investigated the changes in structural and dynamic features of native DNA on binding to the active compound 9. All the synthesized compounds have increased the uptake of Vinblastine in MDR KBCh^R-8-5 cells to an extent of 1.25- to1.9-fold than standard modulator Verapamil of similar concentration. These findings allowed us to draw preliminary conclusions about the structural features of 2-bromoacridones and further chemical enhancement will improve the binding affinity of the acridone derivatives to CT-DNA for better drug–DNA interaction. The molecular modeling studies have shown mechanism of action and the binding modes of the acridones to DNA.     

Changes in Morphology,Anatomy, and Photosynthetic Capacity of Needles of Japanese Larch (Larix kaempferi) Seedlings Grown in High CO2 Concentrations

Photosynthetic traits of two-year-old Japanese larch seedlings (Larix kaempferi Carr.) grown at elevated CO₂ concentrations were studied in relation to structural changes in the needles. Seedlings were grown at two CO₂ concentrations, 360 (AC) and 720 (EC) mol mol^–1 at high and low nutrient supply rates, high N (HN) and low N (LN). The photosynthetic capacity fell significantly in EC+LN, but increased significantly in EC+HN. Since the mesophyll surface area exposed to intercellular space per unit leaf area (A^mes/A) is correlated with the photosynthetic rate, we measured A^mes/A for larch needles growing in EC. Changes of A^mes/A in both EC+HN and EC+LN were very similar to the changes in photosynthetic capacity. This suggests that the changes of A^mes/A in EC probably caused the changes in the photosynthetic capacity. The changes of A^mes/A in EC were attributed to changes in the mesophyll cell size and mesophyll cell number. The photosynthetic capacity in EC can be explained by taking morphological and structural adaptations into account as well as biochemical factors.     

Differential stability of the bovine prion protein upon urea unfolding

Prion diseases, or transmissible spongiform encephalopathies, are a group of infectious neurological diseases associated with the structural conversion of an endogenous protein (PrP) in the central nervous system. There are two major forms of this protein: the native and noninfectious cellular form, PrP^C; and the misfolded, infectious, and proteinase K‐resistant form, PrP^Sc. The C‐terminal domain of PrP^C is mainly α‐helical in structure, whereas PrP^Sc in known to aggregate into an assembly of β‐sheets, forming amyloid fibrils. To identify the regions of PrP^C potentially involved in the initial steps of the conversion to the infectious conformation, we have used high‐resolution NMR spectroscopy to characterize the stability and structure of bovine recombinant PrP^C (residues 121 to 230) during unfolding with the denaturant urea. Analysis of the 800 MHz ¹H NMR spectra reveals region‐specific information about the structural changes occurring upon unfolding. Our data suggest that the dissociation of the native β‐sheet of PrP^C is a primary step in the urea‐induced unfolding process, while strong hydrophobic interactions between helices α1 and α3, and between α2 and α3, stabilize these regions even at very high concentrations of urea.     

Pressure-dependent <Superscript>13</Superscript>C chemical shifts in proteins: origins and applications

Pressure-dependent ¹³C chemical shifts have been measured for aliphatic carbons in barnase and Protein G. Up to 200 MPa (2 kbar), most shift changes are linear, demonstrating pressure-independent compressibilities. CH₃, CH₂ and CH carbon shifts change on average by +0.23, −0.09 and −0.18 ppm, respectively, due to a combination of bond shortening and changes in bond angles, the latter matching one explanation for the γ-gauche effect. In addition, there is a residue-specific component, arising from both local compression and conformational change. To assess the relative magnitudes of these effects, residue-specific shift changes for protein G were converted into structural restraints and used to calculate the change in structure with pressure, using a genetic algorithm to convert shift changes into dihedral angle restraints. The results demonstrate that residual ¹³Cα shifts are dominated by dihedral angle changes and can be used to calculate structural change, whereas ¹³Cβ shifts retain significant dependence on local compression, making them less useful as structural restraints.     

Comparison of Crystal Field Dependent and Independent Methods to Analyse Lanthanide Induced NMR Shifts in Axially Symmetric Complexes. Part II: Systems with a C4 Symmetry Axis

Analysis of the LIS data for several series of Ln³⁺ complexes of C₄ symmetry in terms of structural changes, crystal-field effects and/or variation of hyperfine constants along the lanthanide series was undertaken using a combination of the two-nuclei and three-nuclei techniques together with the classical onenucleus technique. Isostructurality of whole series of complexes, with changes of the F_i, and B₀² parameters, was clearly defined for the complexes of L by the combination of the two first methods. Small changes, involving the three F_i, G_i and B₀² parameters, are observed for the series of complexes of L-L4, using the three data plotting methods. Some of the plots according to the two- and three-nuclei methods are accidentally linear, without necessarily implying isostructurality of the complexes, as they involve parameters, which may be insensitive to any small structural changes occurring in these systems. These parameter variations could result from a magnification, by the present graphical analysis, of the breaks expected from the gradual structural changes along the series due to the lanthanide contraction. The α and β parameters of the three-nuclei method are not diagnostic of the type of structures the complexes have in solution, due to their very indirect dependence on the geometric factors.