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•Chemical exchange methods for application to biomacromolecules are reviewed.•A unified description of spin-locking experiments from weak to strong field limits is ...provided.•Applications to biological processes of folding, recognition and catalysis are highlighted.•Areas for future developments and applications to biological systems are outlined.
The perspective reviews quantitative investigations of chemical exchange phenomena in proteins and other biological macromolecules using NMR spectroscopy, particularly relaxation dispersion methods. The emphasis is on techniques and applications that quantify the populations, interconversion kinetics, and structural features of sparsely populated conformational states in equilibrium with a highly populated ground state. Applications to folding, molecular recognition, catalysis, and allostery by proteins and nucleic acids are highlighted.
Significance Non-native plants dominate global lists of invasive (harmful) species, yet plants introduced to Britain are both less widespread than native species and not increasing any more than ...native plants, and changes to native and non-native plant diversity are positively associated. The hypothesis that competitive exclusion will eventually enable introduced plants to drive native species extinct receives no support, according to analysis of extensive British data. A more parsimonious explanation is that both native and introduced plants are responding predominantly to other drivers of environmental change. The negative effects of non-native plants on British biodiversity have been exaggerated, and may also have been exaggerated in other parts of the world.
Plants are commonly listed as invasive species, presuming that they cause harm at both global and regional scales. Approximately 40% of all species listed as invasive within Britain are plants. However, invasive plants are rarely linked to the national or global extinction of native plant species. The possible explanation is that competitive exclusion takes place slowly and that invasive plants will eventually eliminate native species (the “time-to-exclusion hypothesis”). Using the extensive British Countryside Survey Data, we find that changes to plant occurrence and cover between 1990 and 2007 at 479 British sites do not differ between native and non-native plant species. More than 80% of the plant species that are widespread enough to be sampled are native species; hence, total cover changes have been dominated by native species (total cover increases by native species are more than nine times greater than those by non-native species). This implies that factors other than plant “invasions” are the key drivers of vegetation change. We also find that the diversity of native species is increasing in locations where the diversity of non-native species is increasing, suggesting that high diversities of native and non-native plant species are compatible with one another. We reject the time-to-exclusion hypothesis as the reason why extinctions have not been observed and suggest that non-native plant species are not a threat to floral diversity in Britain. Further research is needed in island-like environments, but we question whether it is appropriate that more than three-quarters of taxa listed globally as invasive species are plants.
The kidney filters vast quantities of Na at the glomerulus but excretes a very small fraction of this Na in the final urine. Although almost every nephron segment participates in the reabsorption of ...Na in the normal kidney, the proximal segments (from the glomerulus to the macula densa) and the distal segments (past the macula densa) play different roles. The proximal tubule and the thick ascending limb of the loop of Henle interact with the filtration apparatus to deliver Na to the distal nephron at a rather constant rate. This involves regulation of both filtration and reabsorption through the processes of glomerulotubular balance and tubuloglomerular feedback. The more distal segments, including the distal convoluted tubule (DCT), connecting tubule, and collecting duct, regulate Na reabsorption to match the excretion with dietary intake. The relative amounts of Na reabsorbed in the DCT, which mainly reabsorbs NaCl, and by more downstream segments that exchange Na for K are variable, allowing the simultaneous regulation of both Na and K excretion.
Palmer describes the principal applications of spin relaxation methods for investigating conformational dynamic processes in proteins and nucleic acids. He focuses on the interpretation of spin ...relaxation data, rather than its acquisition.
Early researchers of radiocarbon levels in Southern Hemisphere tree rings identified a variable North-South hemispheric offset, necessitating construction of a separate radiocarbon calibration curve ...for the South. We present here SHCal20, a revised calibration curve from 0–55,000 cal BP, based upon SHCal13 and fortified by the addition of 14 new tree-ring data sets in the 2140–0, 3520–3453, 3608–3590 and 13,140–11,375 cal BP time intervals. We detail the statistical approaches used for curve construction and present recommendations for the use of the Northern Hemisphere curve (IntCal20), the Southern Hemisphere curve (SHCal20) and suggest where application of an equal mixture of the curves might be more appropriate. Using our Bayesian spline with errors-in-variables methodology, and based upon a comparison of Southern Hemisphere tree-ring data compared with contemporaneous Northern Hemisphere data, we estimate the mean Southern Hemisphere offset to be 36 ± 27 14C yrs older.
Patient-derived xenografts (PDXs) have emerged as an important platform to elucidate new treatments and biomarkers in oncology. PDX models are used to address clinically relevant questions, including ...the contribution of tumour heterogeneity to therapeutic responsiveness, the patterns of cancer evolutionary dynamics during tumour progression and under drug pressure, and the mechanisms of resistance to treatment. The ability of PDX models to predict clinical outcomes is being improved through mouse humanization strategies and the implementation of co-clinical trials, within which patients and PDXs reciprocally inform therapeutic decisions. This Opinion article discusses aspects of PDX modelling that are relevant to these questions and highlights the merits of shared PDX resources to advance cancer medicine from the perspective of EurOPDX, an international initiative devoted to PDX-based research.
Clinical exome sequencing (CES) is rapidly becoming a common molecular diagnostic test for individuals with rare genetic disorders.
To report on initial clinical indications for CES referrals and ...molecular diagnostic rates for different indications and for different test types.
Clinical exome sequencing was performed on 814 consecutive patients with undiagnosed, suspected genetic conditions at the University of California, Los Angeles, Clinical Genomics Center between January 2012 and August 2014. Clinical exome sequencing was conducted as trio-CES (both parents and their affected child sequenced simultaneously) to effectively detect de novo and compound heterozygous variants or as proband-CES (only the affected individual sequenced) when parental samples were not available.
Clinical indications for CES requests, molecular diagnostic rates of CES overall and for phenotypic subgroups, and differences in molecular diagnostic rates between trio-CES and proband-CES.
Of the 814 cases, the overall molecular diagnosis rate was 26% (213 of 814; 95% CI, 23%-29%). The molecular diagnosis rate for trio-CES was 31% (127 of 410 cases; 95% CI, 27%-36%) and 22% (74 of 338 cases; 95% CI, 18%-27%) for proband-CES. In cases of developmental delay in children (<5 years, n = 138), the molecular diagnosis rate was 41% (45 of 109; 95% CI, 32%-51%) for trio-CES cases and 9% (2 of 23, 95% CI, 1%-28%) for proband-CES cases. The significantly higher diagnostic yield (P value = .002; odds ratio, 7.4 95% CI, 1.6-33.1) of trio-CES was due to the identification of de novo and compound heterozygous variants.
In this sample of patients with undiagnosed, suspected genetic conditions, trio-CES was associated with higher molecular diagnostic yield than proband-CES or traditional molecular diagnostic methods. Additional studies designed to validate these findings and to explore the effect of this approach on clinical and economic outcomes are warranted.
Biological activities of enzymes, including regulation or coordination of mechanistic stages preceding or following the chemical step, may depend upon kinetic or equilibrium changes in protein ...conformations. Exchange of more open or flexible conformational states with more closed or constrained states can influence inhibition, allosteric regulation, substrate recognition, formation of the Michaelis complex, side reactions, and product release. NMR spectroscopy has long been applied to the study of conformational dynamic processes in enzymes because these phenomena can be characterized over multiple time scales with atomic site resolution. Laboratory-frame spin-relaxation measurements, sensitive to reorientational motions on picosecond–nanosecond time scales, and rotating-frame relaxation-dispersion measurements, sensitive to chemical exchange processes on microsecond–millisecond time scales, provide information on both conformational distributions and kinetics. This Account reviews NMR spin relaxation studies of the enzymes ribonuclease HI from mesophilic (Escherichia coli) and thermophilic (Thermus thermophilus) bacteria, E. coli AlkB, and Saccharomyces cerevisiae triosephosphate isomerase to illustrate the contributions of conformational flexibility and dynamics to diverse steps in enzyme mechanism. Spin relaxation measurements and molecular dynamics (MD) simulations of the bacterial ribonuclease H enzymes show that the handle region, one of three loop regions that interact with substrates, interconverts between two conformations. Comparison of these conformations with the structure of the complex between Homo sapiens ribonuclease H and a DNA:RNA substrate suggests that the more closed state is inhibitory to binding. The large population of the closed conformation in T. thermophilus ribonuclease H contributes to the increased Michaelis constant compared with the E. coli enzyme. NMR spin relaxation and fluorescence spectroscopy have characterized a conformational transition in AlkB between an open state, in which the side chains of methionine residues in the active site are disordered, and a closed state, in which these residues are ordered. The open state is highly populated in the AlkB/Zn(II) complex, and the closed state is highly populated in the AlkB/Zn(II)/2OG/substrate complex, in which 2OG is the 2-oxoglutarate cosubstrate and the substrate is a methylated DNA oligonucleotide. The equilibrium is shifted to approximately equal populations of the two conformations in the AlkB/Zn(II)/2OG complex. The conformational shift induced by 2OG ensures that 2OG binds to AlkB/Zn(II) prior to the substrate. In addition, the opening rate of the closed conformation limits premature release of substrate, preventing generation of toxic side products by reaction with water. Closure of active site loop 6 in triosephosphate isomerase is critical for forming the Michaelis complex, but reopening of the loop after the reaction is (partially) rate limiting. NMR spin relaxation and MD simulations of triosephosphate isomerase in complex with glycerol 3-phosphate demonstrate that closure of loop 6 is a highly correlated rigid-body motion. The MD simulations also indicate that motions of Gly173 in the most flexible region of loop 6 contribute to opening of the active site loop for product release. Considered together, these three enzyme systems illustrate the power of NMR spin relaxation investigations in providing global insights into the role of conformational dynamic processes in the mechanisms of enzymes from initial activation to final product release.
Nearly 50% of human malignancies exhibit unregulated RAS-ERK signaling; inhibiting it is a valid strategy for antineoplastic intervention. Upon activation, ERK dimerize, which is essential for ERK ...extranuclear, but not for nuclear, signaling. Here, we describe a small molecule inhibitor for ERK dimerization that, without affecting ERK phosphorylation, forestalls tumorigenesis driven by RAS-ERK pathway oncogenes. This compound is unaffected by resistance mechanisms that hamper classical RAS-ERK pathway inhibitors. Thus, ERK dimerization inhibitors provide the proof of principle for two understudied concepts in cancer therapy: (1) the blockade of sub-localization-specific sub-signals, rather than total signals, as a means of impeding oncogenic RAS-ERK signaling and (2) targeting regulatory protein-protein interactions, rather than catalytic activities, as an approach for producing effective antitumor agents.
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•DEL-22379 inhibits ERK dimerization without affecting its phosphorylation.•DEL-22379 blocks proliferation of tumor cells harboring RAS-ERK pathway oncogenes.•In animal tumor models, DEL-22379 induces apoptosis, preventing tumor progression.•DEL-22379 is unaffected by resistance mechanisms that hamper BRAF/MEK inhibitors.
Herrero et al. identify a small molecule inhibitor of ERK dimerization that impedes the growth of tumor cells dependent on a hyperactivated RAS-ERK pathway. Importantly, the antitumor effect of this compound in cells is not affected by the reported resistance mechanisms for the current BRAF and MEK inhibitors.
Simple physical models for restricted diffusion in a potential, which provide important insights for NMR spin relaxation, usually are based on free diffusion within rigid boundaries or diffusion in ...relatively simple continuous potential energy surfaces. The diffusion-in-a-cone model is an example of the former and diffusion in an N-fold cosine potential is an example of the latter. The present work models restricted diffusion for arbitrary potential energy functions on the surface of a cone or a sphere, by expanding the potentials in Fourier or spherical harmonic series, respectively. The results exhibit simple relationships between generalized order parameters and effective correlation times, critical for analysis of experimental spin relaxation data, and illustrate the transition from diffusive-like to jump-like behavior in multi-well potentials.
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•Autocorrelation functions for diffusion in continuous model potentials.•Comparisons to diffusion-in-a-cone and diffusion-on-a-cone models with rigid boundaries.•Transition from diffusive to jump-like behavior in a three-fold unequal-well potential.
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