1
|
Ostrovsky D, Diomina G, Lysak E, Matveeva E, Ogrel O, Trutko S. Effect of oxidative stress on the biosynthesis of 2-C-methyl-D-erythritol-2,4-cyclopyrophosphate and isoprenoids by several bacterial strains. Arch Microbiol 1998; 171:69-72. [PMID: 9871022 DOI: 10.1007/s002030050680] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, the gram-negative bacteria Xanthomonas campestris, Xanthomonas maltophilia, and Pseudomonas putida, facultative parasites of plants and animals, were shown to accumulate 2-C-methyl-d-erythritol-2,4-cyclopyrophosphate (MEC) in response to benzyl-viologen-induced oxidative stress. Corynebacterium ammoniagenes mutants capable of accumulating MEC in the absence of an exogenous oxidative stress inducer were obtained. Isoprenoid synthesis and MEC synthesis in these and other bacteria were shown to be alternative processes, while biosynthesis of brominated polyene xanthomonadin (an antioxidant pigment of X. campestris) increased concomitantly with the accumulation of MEC.
Collapse
|
Comparative Study |
27 |
49 |
2
|
Vugmeyster L, Ostrovsky D, Ford JJ, Burton SD, Lipton AS, Hoatson GL, Vold RL. Probing the dynamics of a protein hydrophobic core by deuteron solid-state nuclear magnetic resonance spectroscopy. J Am Chem Soc 2009; 131:13651-8. [PMID: 19772361 DOI: 10.1021/ja902977u] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
With the goal of investigating dynamical features of hydrophobic cores of proteins over a wide range of temperatures, the chicken villin headpiece subdomain protein (HP36) was labeled at a "single" site corresponding to any one of the two C(delta)D(3) groups of leucine-69, which is located in a key position of the core. The main techniques employed are deuteron NMR quadrupolar echo line shape analysis, and T(1Z) (Zeeman) and T(1Q) (quadrupolar order) relaxation experiments performed at 11.7 and 17.6 T over the temperature range of 112 to 298 K. The experimental data are compared with computer simulations. The deuteron line shapes give an excellent fit to a three-mode motional model that consists of (a) fast three-site rotational jumps about the pseudo C(3) methyl spinning axis, (b) slower reorientation of the spinning axis, described by diffusion along a restricted arc, and (c) large angle jumps between traces of rotameric conformers. Relaxation behavior is described by a phenomenological distribution of activation energies for three-site hops at high temperatures that collapses to a single, distinctly smaller value for lower temperatures.
Collapse
|
Research Support, U.S. Gov't, Non-P.H.S. |
16 |
42 |
3
|
Vugmeyster L, Clark MA, Falconer IB, Ostrovsky D, Gantz D, Qiang W, Hoatson GL. Flexibility and Solvation of Amyloid-β Hydrophobic Core. J Biol Chem 2016; 291:18484-95. [PMID: 27402826 DOI: 10.1074/jbc.m116.740530] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Indexed: 11/06/2022] Open
Abstract
Amyloid fibril deposits found in Alzheimer disease patients are composed of amyloid-β (Aβ) protein forming a number of hydrophobic interfaces that are believed to be mostly rigid. We have investigated the μs-ms time-scale dynamics of the intra-strand hydrophobic core and interfaces of the fibrils composed of Aβ1-40 protein. Using solid-state (2)H NMR line shape experiments performed on selectively deuterated methyl groups, we probed the 3-fold symmetric and 2-fold symmetric polymorphs of native Aβ as well as the protofibrils of D23N Iowa mutant, associated with an early onset of Alzheimer disease. The dynamics of the hydrophobic regions probed at Leu-17, Leu-34, Val-36, and Met-35 side chains were found to be very pronounced at all sites and in all polymorphs of Aβ, with methyl axis motions persisting down to 230-200 K for most of the sites. The dominant mode of motions is the rotameric side chain jumps, with the Met-35 displaying the most complex multi-modal behavior. There are distinct differences in the dynamics among the three protein variants, with the Val-36 site displaying the most variability. Solvation of the fibrils does not affect methyl group motions within the hydrophobic core of individual cross-β subunits but has a clear effect on the motions at the hydrophobic interface between the cross-β subunits, which is defined by Met-35 contacts. In particular, hydration activates transitions between additional rotameric states that are not sampled in the dry protein. Thus, these results support the existence of water-accessible cavity recently predicted by molecular dynamics simulations and suggested by cryo-EM studies.
Collapse
|
Research Support, N.I.H., Extramural |
9 |
40 |
4
|
Hu ZW, Vugmeyster L, Au DF, Ostrovsky D, Sun Y, Qiang W. Molecular structure of an N-terminal phosphorylated β-amyloid fibril. Proc Natl Acad Sci U S A 2019; 116:11253-11258. [PMID: 31097588 PMCID: PMC6561245 DOI: 10.1073/pnas.1818530116] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The structural polymorphism in β-amyloid (Aβ) plaques from Alzheimer disease (AD) has been recognized as an important pathological factor. Plaques from sporadic AD patients contain fibrillar deposits of various amyloid proteins/peptides, including posttranslational modified Aβ (PTM-Aβ) subtypes. Although many PTM-Aβs were shown to accelerate the fibrillation process, increase neuronal cytotoxicity of aggregates, or enhance the stability of fibrils, the contribution of PTM-Aβs to structural polymorphisms and their pathological roles remains unclear. We report here the NMR-based structure for the Ser-8-phosphorylated 40-residue Aβ (pS8-Aβ40) fibrils, which shows significant difference to the wild-type fibrils, with higher cross-seeding efficiency and thermodynamic stability. Given these physicochemical properties, the structures originated from pS8-Aβ40 fibrils may potentially dominate the polymorphisms in the mixture of wild-type and phosphorylated Aβ deposits. Our results imply that Aβ subtypes with "seeding-prone" properties may influence the polymorphisms of amyloid plaques through the cross-seeding process.
Collapse
|
research-article |
6 |
40 |
5
|
Lash JW, Seitz AW, Cheney CM, Ostrovsky D. On the role of fibronectin during the compaction stage of somitogenesis in the chick embryo. THE JOURNAL OF EXPERIMENTAL ZOOLOGY 1984; 232:197-206. [PMID: 6389752 DOI: 10.1002/jez.1402320207] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
During the early stages of somitogenesis in the chick embryo the presomitic cells in the segmental plate undergo compaction. The aggregation of segmental plate cells is stimulated by fibronectin. The stimulation of segmental plate cells to aggregate and undergo compaction can be effected in isolated segmental plate cells, in isolated segmental plates, and in intact embryos removed from the yolk. The fact that the segmental plate cells react with greater vigor to cellular fibronectin than to plasma fibronectin suggests a specific molecular mechanism in the initiation of somitogenesis.
Collapse
|
|
41 |
38 |
6
|
Vugmeyster L, Ostrovsky D, Khadjinova A, Ellden J, Hoatson GL, Vold RL. Slow motions in the hydrophobic core of chicken villin headpiece subdomain and their contributions to configurational entropy and heat capacity from solid-state deuteron NMR measurements. Biochemistry 2011; 50:10637-46. [PMID: 22085262 PMCID: PMC3366553 DOI: 10.1021/bi201515b] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have investigated microsecond to millisecond time scale dynamics in several key hydrophobic core methyl groups of chicken villin headpiece subdomain protein (HP36) using a combination of single-site labeling, deuteron solid-state NMR line shape analysis, and computational modeling. Deuteron line shapes of hydrated powder samples are dominated by rotameric jumps and show a large variability of rate constants, activation energies, and rotameric populations. Site-specific activation energies vary from 6 to 38 kJ/mol. An additional mode of diffusion on a restricted arc is significant for some sites. In dry samples, the dynamics is quenched. Parameters of the motional models allow for calculations of configurational entropy and heat capacity, which, together with the rate constants, allow for observation of interplay between thermodynamic and kinetic picture of the landscape. Mutations at key phenylalanine residues at both distal (F47L&F51L) and proximal (F58L) locations to a relatively rigid side chain of L69 have a pronounced effect on alleviating the rigidity of this side chain at room temperature and demonstrate the sensitivity of the hydrophobic core environment to such perturbations.
Collapse
|
Research Support, N.I.H., Extramural |
14 |
37 |
7
|
Ostrovsky D, Cheney CM, Seitz AW, Lash JW. Fibronectin distribution during somitogenesis in the chick embryo. CELL DIFFERENTIATION 1983; 13:217-23. [PMID: 6667497 DOI: 10.1016/0045-6039(83)90092-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Somite formation in vertebrates is a multi-stage process. From a relatively homogeneous rod of mesenchyme, the segmental plate, somites are formed in a repeating sequence. Cell-cell adhesion has been proposed as a causal factor in somitogenesis. This led to an analysis of fibronectin in the segmental plate with respect to the initiation of somitogenesis. The pattern of fibronectin distribution can be correlated with the initiation of somitogenesis in the anterior portion of the segmental plate. Fibronectin distribution was determined using a high resolution antibody localization technique. Differences in fibronectin distribution were verified with computer-assisted image analysis. The evidence presented supports the hypothesis that an increase in cell-cell adhesion is a significant factor in the initiation of somitogenesis.
Collapse
|
Comparative Study |
42 |
35 |
8
|
Vugmeyster L, Ostrovsky D, Ford JJ, Lipton AS. Freezing of dynamics of a methyl group in a protein hydrophobic core at cryogenic temperatures by deuteron NMR spectroscopy. J Am Chem Soc 2010; 132:4038-9. [PMID: 20201523 DOI: 10.1021/ja909599k] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Methyl groups are thought to dominate the dynamics of proteins after slow collective modes of motion freeze out in a glass-transition process. In this work we investigate methyl group dynamics of a key hydrophobic core leucine residue in chicken villin headpiece subdomain protein at 140-4 K using deuteron NMR longitudinal relaxation measurements. A distinct increase in the apparent activation energy is observed at approximately 95 K, indicating an abrupt freezing of methyl group dynamics. Relaxation times at temperatures below 60 K are dominated by the deuteron tunneling mechanism.
Collapse
|
Research Support, Non-U.S. Gov't |
15 |
29 |
9
|
Vold RL, Hoatson GL, Vugmeyster L, Ostrovsky D, De Castro PJ. Solid state deuteron relaxation time anisotropy measured with multiple echo acquisition. Phys Chem Chem Phys 2009; 11:7008-12. [PMID: 19652835 DOI: 10.1039/b907343d] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The signal to noise ratio of solid state deuteron NMR line shapes can be significantly improved by recording multiple echoes, generated either by a quadrupole Carr-Purcell-Meiboom-Gill pulse train (QCPMG) or by magic angle spinning (MAS). It is shown in this article, theoretically and experimentally, that when these techniques are used to record partially relaxed spectra, the relaxation times of Zeeman order, T(1Z), and quadrupole order, T(1Q), measured for individual side bands in QCPMG experiments preserve relaxation time anisotropy, while rotational side bands in MAS spectra do not. The relaxation times of individual QCPMG sidebands are not identical to those measured at the same frequencies on partially relaxed quadrupole echo powder patterns, and must be computed by explicit simulation.
Collapse
|
Research Support, U.S. Gov't, Non-P.H.S. |
16 |
28 |
10
|
Vugmeyster L, Ostrovsky D. Static solid-state 2H NMR methods in studies of protein side-chain dynamics. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 101:1-17. [PMID: 28844219 PMCID: PMC5576518 DOI: 10.1016/j.pnmrs.2017.02.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 02/15/2017] [Accepted: 02/17/2017] [Indexed: 05/27/2023]
Abstract
In this review, we discuss the experimental static deuteron NMR techniques and computational approaches most useful for the investigation of side-chain dynamics in protein systems. Focus is placed on the interpretation of line shape and relaxation data within the framework of motional modeling. We consider both jump and diffusion models and apply them to uncover glassy behaviors, conformational exchange and dynamical transitions in proteins. Applications are chosen from globular and membrane proteins, amyloid fibrils, peptide adsorbed on surfaces and proteins specific to connective tissues.
Collapse
|
Research Support, N.I.H., Extramural |
8 |
27 |
11
|
Vugmeyster L, Ostrovsky D, Penland K, Hoatson GL, Vold RL. Glassy dynamics of protein methyl groups revealed by deuteron NMR. J Phys Chem B 2013; 117:1051-61. [PMID: 23301823 DOI: 10.1021/jp311112j] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We investigated site-specific dynamics of key methyl groups in the hydrophobic core of chicken villin headpiece subdomain (HP36) over the temperature range between 298 and 140 K using deuteron solid-state NMR longitudinal relaxation measurements. The relaxation of the longitudinal magnetization is weakly nonexponential (glassy) at high temperatures and exhibits a stronger degree of nonexponentiality below about 175 K. In addition, the characteristic relaxation times deviate from the simple Arrhenius law. We interpret this behavior via the existence of distribution of activation energy barriers for the three-site methyl jumps, which originates from somewhat different methyl environments within the local energy landscape. The width of the distribution of the activation barriers for methyl jumps is rather significant, about 1.4 kJ/mol. Our experimental results and modeling allow for the description of the apparent change at about 175 K without invoking a specific transition temperature. For most residues in the core, the relaxation behavior at high temperatures points to the existence of conformational exchange between the substates of the landscape, and our model takes into account the kinetics of this process. The observed dynamics are the same for dry and hydrated protein. We also looked at the effect of F58L mutation inside the hydrophobic core on the dynamics of one of the residues and observed a significant increase in its conformational exchange rate constant at high temperatures.
Collapse
|
Research Support, U.S. Gov't, Non-P.H.S. |
12 |
24 |
12
|
Au DF, Ostrovsky D, Fu R, Vugmeyster L. Solid-state NMR reveals a comprehensive view of the dynamics of the flexible, disordered N-terminal domain of amyloid-β fibrils. J Biol Chem 2019; 294:5840-5853. [PMID: 30737281 DOI: 10.1074/jbc.ra118.006559] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 02/08/2019] [Indexed: 11/06/2022] Open
Abstract
Amyloid fibril deposits observed in Alzheimer's disease comprise amyloid-β (Aβ) protein possessing a structured hydrophobic core and a disordered N-terminal domain (residues 1-16). The internal flexibility of the disordered domain is likely essential for Aβ aggregation. Here, we used 2H static solid-state NMR methods to probe the dynamics of selected side chains of the N-terminal domain of Aβ1-40 fibrils. Line shape and relaxation data suggested a two-state model in which the domain's free state undergoes a diffusive motion that is quenched in the bound state, likely because of transient interactions with the structured C-terminal domain. At 37 °C, we observed freezing of the dynamics progressively along the Aβ sequence, with the fraction of the bound state increasing and the rate of diffusion decreasing. We also found that without solvation, the diffusive motion is quenched. The solvent acted as a plasticizer reminiscent of its role in the onset of global dynamics in globular proteins. As the temperature was lowered, the fraction of the bound state exhibited sigmoidal behavior. The midpoint of the freezing curve coincided with the bulk solvent freezing for the N-terminal residues and increased further along the sequence. Using 2H R 1ρ measurements, we determined the conformational exchange rate constant between the free and bound states under physiological conditions. Zinc-induced aggregation leads to the enhancement of the dynamics, manifested by the faster conformational exchange, faster diffusion, and lower freezing-curve midpoints.
Collapse
|
Research Support, U.S. Gov't, Non-P.H.S. |
6 |
21 |
13
|
Vugmeyster L, Ostrovsky D, Villafranca T, Sharp J, Xu W, Lipton AS, Hoatson GL, Vold RL. Dynamics of Hydrophobic Core Phenylalanine Residues Probed by Solid-State Deuteron NMR. J Phys Chem B 2015; 119:14892-904. [PMID: 26529128 PMCID: PMC4970646 DOI: 10.1021/acs.jpcb.5b09299] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We conducted a detailed investigation of the dynamics of two phenylalanine side chains in the hydrophobic core of the villin headpiece subdomain protein (HP36) in the hydrated powder state over the 298-80 K temperature range. Our main tools were static deuteron NMR measurements of longitudinal relaxation and line shapes supplemented with computational modeling. The temperature dependence of the relaxation times reveals the presence of two main mechanisms that can be attributed to the ring-flips, dominating at high temperatures, and small-angle fluctuations, dominating at low temperatures. The relaxation is nonexponential at all temperatures with the extent of nonexponentiality increasing from higher to lower temperatures. This behavior suggests a distribution of conformers with unique values of activation energies. The central values of the activation energies for the ring-flipping motions are among the smallest reported for aromatic residues in peptides and proteins and point to a very mobile hydrophobic core. The analysis of the widths of the distributions, in combination with the earlier results on the dynamics of flanking methyl groups (Vugmeyster et al. J. Phys. Chem. B 2013, 117, 6129-6137), suggests that the hydrophobic core undergoes slow concerted fluctuations. There is a pronounced effect of dehydration on the ring-flipping motions, which shifts the distribution toward more rigid conformers. The crossover temperature between the regions of dominance of the small-angle fluctuations and ring-flips shifts from 195 K in the hydrated protein to 278 K in the dry one. This result points to the role of solvent in softening the core and highlights aromatic residues as markers of the protein dynamical transitions.
Collapse
|
Research Support, N.I.H., Extramural |
10 |
19 |
14
|
Abstract
This report describes the initiation of somitogenesis in the mouse embryo. Correlations are made with fibronectin distribution around the unsegmented mesoderm and the distribution of cytoskeletal elements within the cells as they undergo morphogenetic movements. The same temporal and topological changes in fibronectin, laminin, and cytoskeletal elements are seen in mouse somitogenesis as in the chick embryo. A notable exception is that the epithelial stage of somitogenesis in the mouse does not form a closed vesicle as it does in the chick. In the mouse the mesial portion of the forming somite does not become epithelial before the migration of sclerotomal cells.
Collapse
|
|
37 |
18 |
15
|
Ostrovsky D, Shipanova I, Sibeldina L, Shashkov A, Kharatian E, Malyarova I, Tantsyrev G. A new cyclopyrophosphate as a bacterial antistressor? FEBS Lett 1992; 298:159-61. [PMID: 1312021 DOI: 10.1016/0014-5793(92)80045-i] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
In a number of bacteria an unusual glycosyl pyrophosphate (31P NMR signal chemical shift at about -15 ppm) was detected when the cells were subjected to oxidative stress. This substance from Brevibacterium ammoniagenes has now been identified as 2-methyl-butan-1,2,3,4,-tetraol-2,4-cyclopyrophosphate, which is accumulated in the cell under certain conditions in concentrations of of about 50 mM. It is now suggested that this compound is the long sought after bacterial antistressor.
Collapse
|
|
33 |
18 |
16
|
Ostrovsky D, Shashkov A, Sviridov A. Bacterial oxidative-stress substance is 2-C-methyl-D-erythritol 2,4-cyclopyrophosphate. Biochem J 1993; 295 ( Pt 3):901-2. [PMID: 8240308 PMCID: PMC1134649 DOI: 10.1042/bj2950901] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
|
letter |
32 |
16 |
17
|
Ostrovsky D, Sen S, Smeby RR, Bumpus FM. Chemical assay of phospholipid renin preinhibitor in canine and human blood. Circ Res 1967; 21:497-505. [PMID: 4293657 DOI: 10.1161/01.res.21.4.497] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A phospholipid previously shown to be converted to a lysophospholipid renin inhibitor has been demonstrated in the plasma and red cells of man and the dog. This inhibitor precursor, designated preinhibitor, is chromatographically identical to the compound previously isolated from kidneys of dogs and hogs. A method for its quantitative measurement in plasma and red cells is presented. Normal dogs tested so far have an average of 119.6 µg of preinhibitor phospholipid/ml of blood; 16.3 µg of this is in the plasma. These concentrations are constant (in red cells even increased) 48 hr after bilateral nephrectomy. To assess the physiological importance of preinhibitor, it may be necessary to measure its active lyso derivative as well as the lipase(s) most directly involved in maintaining blood levels of these two phospholipids.
Collapse
|
|
58 |
16 |
18
|
Vugmeyster L, Au DF, Ostrovsky D, Kierl B, Fu R, Hu ZW, Qiang W. Effect of Post-Translational Modifications and Mutations on Amyloid-β Fibrils Dynamics at N Terminus. Biophys J 2019; 117:1524-1535. [PMID: 31570231 PMCID: PMC6817547 DOI: 10.1016/j.bpj.2019.09.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 09/01/2019] [Accepted: 09/09/2019] [Indexed: 02/04/2023] Open
Abstract
We investigate the variability in the dynamics of the disordered N-terminal domain of amyloid-β fibrils (Aβ), comprising residues 1-16 of Aβ1-40, due to post-translational modifications and mutations in the β-bend regions known to modulate aggregation properties. Using 2H static solid-state NMR approaches, we compare the dynamics in the wild-type Aβ fibrils in the threefold symmetric polymorph with the fibrils from three post-translational modification sequences: isoaspartate-D7, the phosphorylation of S8, and an N-terminal truncation ΔE3. Additional comparisons are made with the mutants in the β-bend region (residues 21-23) corresponding to the familial Osaka E22Δ deletion and D23N Iowa mutation. We also include the aggregates induced by Zn2+ ions. The dynamics are probed at the F4 and G9 positions. The main motional model involves two free states undergoing diffusion and conformational exchanges with the bound state in which the diffusion is quenched because of transient interactions involving fibril core and other intrastrand contacts. The fraction of the bound state increases in a sigmoidal fashion with a decrease in temperature. There is clear variability in the dynamics: the phosphorylation of S8 variant is the most rigid at the G9 site in line with structural studies, the ΔE3 fibrils are more flexible at the G9 site in line with the morphological fragmentation pattern, the Zn-induced aggregates are the most mobile, and the two β-bend mutants have the strongest changes at the F4 site toward higher rigidity. Overall, the changes underlie the potential role of conformational ensembles in setting the stage for aggregation-prone states.
Collapse
|
Research Support, N.I.H., Extramural |
6 |
16 |
19
|
Ostrovsky D, Shuryak E. Instanton-induced azimuthal spin asymmetry in deep inelastic scattering. Int J Clin Exp Med 2005. [DOI: 10.1103/physrevd.71.014037] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
|
20 |
16 |
20
|
Vugmeyster L, Ostrovsky D, Hoatson GL, Qiang W, Falconer IB. Solvent-Driven Dynamical Crossover in the Phenylalanine Side-Chain from the Hydrophobic Core of Amyloid Fibrils Detected by 2H NMR Relaxation. J Phys Chem B 2017; 121:7267-7275. [PMID: 28699757 PMCID: PMC5567839 DOI: 10.1021/acs.jpcb.7b04726] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Aromatic residues are important markers of dynamical changes in proteins' hydrophobic cores. In this work we investigated the dynamics of the F19 side-chain in the core of amyloid fibrils across a wide temperature range of 300 to 140 K. We utilized solid-state 2H NMR relaxation to demonstrate the presence of a solvent-driven dynamical crossover between different motional regimes, often also referred to as the dynamical transition. In particular, the dynamics are dominated by small-angle fluctuations at low temperatures and by π-flips of the aromatic ring at high temperatures. The crossover temperature is more than 43 degrees lower for the hydrated state of the fibrils compared to the dry state, indicating that interactions with water facilitate π-flips. Further, crossover temperatures are shown to be very sensitive to polymorphic states of the fibrils, such as the 2-fold and 3-fold symmetric morphologies of the wild-type protein as well as D23N mutant protofibrils. We speculate that these differences can be attributed, at least partially, to enhanced interactions with water in the 3-fold polymorph, which has been shown to have a water-accessible cavity. Combined with previous studies of methyl group dynamics, the results highlight the presence of multiple dynamics modes in the core of the fibrils, which was originally believed to be quite rigid.
Collapse
|
Research Support, N.I.H., Extramural |
8 |
13 |
21
|
Vugmeyster L, Ostrovsky D, Clark MA, Falconer IB, Hoatson GL, Qiang W. Fast Motions of Key Methyl Groups in Amyloid-β Fibrils. Biophys J 2016; 111:2135-2148. [PMID: 27851938 PMCID: PMC5113154 DOI: 10.1016/j.bpj.2016.10.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/18/2016] [Accepted: 10/05/2016] [Indexed: 11/28/2022] Open
Abstract
Amyloid-β (Aβ) peptide is the major component of plaques found in Alzheimer's disease patients. Using solid-state 2H NMR relaxation performed on selectively deuterated methyl groups, we probed the dynamics in the threefold symmetric and twofold symmetric polymorphs of native Aβ as well as the protofibrils of the D23N mutant. Specifically, we investigated the methyl groups of two leucine residues that belong to the hydrophobic core (L17 and L34) as well as M35 residues belonging to the hydrophobic interface between the cross-β subunits, which has been previously found to be water-accessible. Relaxation measurements performed over 310-140 K and two magnetic field strengths provide insights into conformational variability within and between polymorphs. Core packing variations within a single polymorph are similar to what is observed for globular proteins for the core residues, whereas M35 exhibits a larger degree of variability. M35 site is also shown to undergo a solvent-dependent dynamical transition in which slower amplitude motions of methyl axes are activated at high temperature. The motions, modeled as a diffusion of methyl axis, have activation energy by a factor of 2.7 larger in the twofold compared with the threefold polymorph, whereas D23N protofibrils display a value similar to the threefold polymorph. This suggests enhanced flexibility of the hydrophobic interface in the threefold polymorph. This difference is only observed in the hydrated state and is absent in the dry fibrils, highlighting the role of solvent at the cavity. In contrast, the dynamic behavior of the core is hydration-independent.
Collapse
|
research-article |
9 |
13 |
22
|
Vugmeyster L, Au DF, Ostrovsky D, Fu R. Deuteron Solid-State NMR Relaxation Measurements Reveal Two Distinct Conformational Exchange Processes in the Disordered N-Terminal Domain of Amyloid-β Fibrils. Chemphyschem 2019; 20:1680-1689. [PMID: 31087613 PMCID: PMC6663588 DOI: 10.1002/cphc.201900363] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/12/2019] [Indexed: 12/26/2022]
Abstract
We employed deuterium solid-state NMR techniques under static conditions to discern the details of the μs-ms timescale motions in the flexible N-terminal subdomain of Aβ1-40 amyloid fibrils, which spans residues 1-16. In particular, we utilized a rotating frame (R1ρ ) and the newly developed time domain quadrupolar Carr-Purcell-Meiboom-Gill (QCPMG) relaxation measurements at the selectively deuterated side chains of A2, H6, and G9. The two experiments are complementary in terms of probing somewhat different timescales of motions, governed by the tensor parameters and the sampling window of the magnetization decay curves. The results indicated two mobile "free" states of the N-terminal domain undergoing global diffusive motions, with isotropic diffusion coefficients of 0.7-1 ⋅ 108 and 0.3-3 ⋅ 106 ad2 s-1 . The free states are also involved in the conformational exchange with a single bound state, in which the diffusive motions are quenched, likely due to transient interactions with the structured hydrophobic core. The conformational exchange rate constants are 2-3 ⋅ 105 s-1 and 2-3 ⋅ 104 s-1 for the fast and slow diffusion free states, respectively.
Collapse
|
Research Support, N.I.H., Extramural |
6 |
13 |
23
|
Vugmeyster L, Ostrovsky D. Basic experiments in 2H static NMR for the characterization of protein side-chain dynamics. Methods 2018; 148:136-145. [PMID: 29705208 PMCID: PMC6133770 DOI: 10.1016/j.ymeth.2018.04.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/02/2018] [Accepted: 04/24/2018] [Indexed: 12/23/2022] Open
Abstract
The focus of this review is the basic methodology for applications of static deuteron NMR for studies of dynamics in the side chains of proteins. We review experimental approaches for the measurements of static line shapes and relaxation rates as well as signal enhancement strategies using the multiple echo acquisition scheme. Further, we describe computational strategies for modeling jump and diffusive motions underlying experimental data. Applications are chosen from studies of amyloid fibrils comprising the amyloid-β protein.
Collapse
|
Research Support, N.I.H., Extramural |
7 |
12 |
24
|
Vugmeyster L, Ostrovsky D. Temperature dependence of fast carbonyl backbone dynamics in chicken villin headpiece subdomain. JOURNAL OF BIOMOLECULAR NMR 2011; 50:119-27. [PMID: 21416162 PMCID: PMC3366550 DOI: 10.1007/s10858-011-9500-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 03/02/2011] [Indexed: 05/03/2023]
Abstract
Temperature-dependence of protein dynamics can provide information on details of the free energy landscape by probing the characteristics of the potential responsible for the fluctuations. We have investigated the temperature-dependence of picosecond to nanosecond backbone dynamics at carbonyl carbon sites in chicken villin headpiece subdomain protein using a combination of three NMR relaxation rates: (13)C' longitudinal rate, and two cross-correlated rates involving dipolar and chemical shift anisotropy (CSA) relaxation mechanisms, (13)C'/(13)C'-(13)C(α) CSA/dipolar and (13)C'/(13)C'-(15)N CSA/dipolar. Order parameters have been extracted using the Lipari-Szabo model-free approach assuming a separation of the time scales of internal and molecular motions in the 2-16°C temperature range. There is a gradual deviation from this assumption from lower to higher temperatures, such that above 16°C the separation of the time scales is inconsistent with the experimental data and, thus, the Lipari-Szabo formalism can not be applied. While there are variations among the residues, on the average the order parameters indicate a markedly steeper temperature dependence at backbone carbonyl carbons compared to that probed at amide nitrogens in an earlier study. This strongly advocates for probing sites other than amide nitrogen for accurate characterization of the potential and other thermodynamics characteristics of protein backbone.
Collapse
|
Research Support, N.I.H., Extramural |
14 |
11 |
25
|
Lash JW, Gosfield E, Ostrovsky D, Bellairs R. Migration of chick blastoderm under the vitelline membrane: the role of fibronectin. Dev Biol 1990; 139:407-16. [PMID: 2338175 DOI: 10.1016/0012-1606(90)90309-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In the earliest stages of its development the chick blastoderm is a flattened disc at the surface of the yolk. It gradually increases in diameter, partially because the cells are rapidly proliferating, but also because the cells at the periphery (the margin of overgrowth) are migrating in a centrifugal direction. These cells utilize the inner surface of the vitelline membrane as their substratum. In the normal blastoderm, these cells at the edge of the spreading blastoderm are the only cells which are attached to the vitelline membrane. This investigation is concerned with the possible role played by fibronectin in the interaction between these migrating cells and the vitelline membrane. Chick blastoderms, explanted by the New (1955) technique have been treated with synthetic peptides that mimic the adhesive recognition signal of the fibronectin molecule. The pentapeptide GRGDS (containing the specific RGD cell adhesion sequence) caused the edge cells of the blastoderm to detach within minutes, and the expansion of the blastoderm was inhibited for about 4 hr. After this period there was gradual recovery and the cells reattached and spreading resumed. Examination of the margin of the blastoderm by scanning electron microscopy showed that cell processes were lost soon after treatment with GRGDS but concomitant with reattachment and the resumption of spreading, the cell processes reformed. The pentapeptide GRDGS (with the amino acids G and D inverted) produced a brief inhibition of spreading, but after an hour these blastoderms spread at the same rate as controls. Immunocytochemical staining with anti-fibronectin demonstrated that fibronectin was not only present at the interface of the edge cells and the vitelline membrane, but also between the epiblast and the hypoblast. These results indicate that tissue movement during blastoderm spreading is dependent upon fibronectin and that the specific RGD amino acid sequence, and presumably the VLA/integrin family of receptors, is involved in this embryonic morphogenetic movement.
Collapse
|
|
35 |
11 |