Enhanced conformational space sampling improves the prediction of chemical shifts in proteins.

A biased-potential molecular dynamics simulation method, accelerated molecular dynamics (AMD), was combined with the chemical shift prediction algorithm SHIFTX to calculate (1)H(N), (15)N, (13)Calpha, (13)Cbeta, and (13)C' chemical shifts of the ankyrin repeat protein IkappaBalpha (residues 67-206), the primary inhibitor of nuclear factor kappa-B (NF-kappaB). Free-energy-weighted molecular ensembles were generated over a range of acceleration levels, affording systematic enhancement of the conformational space sampling of the protein. We have found that the predicted chemical shifts, particularly for the (15)N, (13)Calpha, and (13)Cbeta nuclei, improve substantially with enhanced conformational space sampling up to an optimal acceleration level. Significant improvement in the predicted chemical shift data coincides with those regions of the protein that exhibit backbone dynamics on longer time scales. Interestingly, the optimal acceleration level for reproduction of the chemical shift data has previously been shown to best reproduce the experimental residual dipolar coupling (RDC) data for this system, as both chemical shift data and RDCs report on an ensemble and time average in the millisecond range

Functional dynamics of the folded ankyrin repeats of I kappa B alpha revealed by nuclear magnetic resonance.

Inhibition of nuclear factor kappaB (NF-kappaB) is mainly accomplished by IkappaB alpha, which consists of a signal response sequence at the N-terminus, a six-ankyrin repeat domain (ARD) that binds NF-kappaB, and a C-terminal PEST sequence. Previous studies with the ARD revealed that the fifth and sixth repeats are only partially folded in the absence of NF-kappaB. Here we report NMR studies of a truncated version of IkappaB alpha, containing only the first four ankyrin repeats, IkappaB alpha(67-206). This four-repeat segment is well-structured in the free state, enabling full resonance assignments to be made. H-D exchange, backbone dynamics, and residual dipolar coupling (RDC) experiments reveal regions of flexibility. In addition, regions consistent with the presence of micro- to millisecond motions occur periodically throughout the repeat structure. Comparison of the RDCs with the crystal structure gave only moderate agreement, but an ensemble of structures generated by accelerated molecular dynamics gave much better agreement with the measured RDCs. The regions showing flexibility correspond to those implicated in entropic compensation for the loss of flexibility in ankyrin repeats 5 and 6 upon binding to NF-kappaB. The regions showing micro- to millisecond motions in the free protein are the ends of the beta-hairpins that directly interact with NF-kappaB in the complex

The Dynamic Structure of Thrombin in Solution

AbstractThe backbone dynamics of human α-thrombin inhibited at the active site serine were analyzed using R1, R2, and heteronuclear NOE experiments, variable temperature TROSY 2D [1H-15N] correlation spectra, and Rex measurements. The N-terminus of the heavy chain, which is formed upon zymogen activation and inserts into the protein core, is highly ordered, as is much of the double beta-barrel core. Some of the surface loops, by contrast, remain very dynamic with order parameters as low as 0.5 indicating significant motions on the ps-ns timescale. Regions of the protein that were thought to be dynamic in the zymogen and to become rigid upon activation, in particular the γ-loop, the 180s loop, and the Na+ binding site have order parameters below 0.8. Significant Rex was observed in most of the γ-loop, in regions proximal to the light chain, and in the β-sheet core. Accelerated molecular dynamics simulations yielded a molecular ensemble consistent with measured residual dipolar couplings that revealed dynamic motions up to milliseconds. Several regions, including the light chain and two proximal loops, did not appear highly dynamic on the ps-ns timescale, but had significant motions on slower timescales

Cardiovascular Health in Anxiety or Mood Problems Study (CHAMPS): study protocol for a randomized controlled trial

Background: Previous psychological and pharmacological interventions have primarily focused on depression disorders in populations with cardiovascular diseases (CVDs) and the efficacy of anxiety disorder interventions is only more recently being explored. Transdiagnostic interventions address common emotional processes and the full range of anxiety and depression disorders often observed in populations with CVDs. The aim of CHAMPS is to evaluate the feasibility of a unified protocol (UP) for the transdiagnostic treatment of emotional disorders intervention in patients recently hospitalized for CVDs. The current study reports the protocol of a feasibility randomized controlled trial to inform a future trial. Methods/Design: This is a feasibility randomized, controlled trial with a single-center design. A total of 50 participants will be block-randomized to either a UP intervention or enhanced usual care. Both groups will receive standard CVD care. The UP intervention consists of 1) enhancing motivation, readiness for change, and treatment engagement; (2) psychoeducation about emotions; (3) increasing present focused emotion awareness; (4) increasing cognitive flexibility; (5) identifying and preventing patterns of emotion avoidance and maladaptive emotion-driven behaviors (EDBs, including tobacco smoking, and alcohol use); (6) increasing tolerance of emotion-related physical sensations; (7) interoceptive and situation-based emotion-focused exposure; and (8) relapse prevention strategies. Treatment duration is 12 to 18 weeks. Relevant outcomes include the standard deviation of self-rated anxiety, depression and quality of life symptoms. Other outcomes include intervention acceptability, satisfaction with care, rates of EDBs, patient adherence, physical activity, cardiac and psychiatric readmissions. Parallel to the main trial, a nonrandomized comparator cohort will be recruited comprising 150 persons scoring below the predetermined depression and anxiety severity thresholds. Discussion: CHAMPS is designed to evaluate the UP for the transdiagnostic treatment of emotional disorders targeting emotional disorder processes in a CVD population. The design will provide preliminary evidence of feasibility, attrition, and satisfaction with treatment to design a definitive trial. If the trial is feasible, it opens up the possibility for interventions to target broader emotional processes in the precarious population with CVD and emotional distress

Hadley circulation and precipitation changes control black shale deposition in the Late Jurassic Boreal Seaway

New climate simulations using the HadCM3L model with a paleogeography of the Late Jurassic [155.5 Ma], and proxy-data corroborate that warm and wet tropical-like conditions reached as far north as the UK sector of the Jurassic Boreal Seaway [~35oN]. This is associated with a northern hemisphere Jurassic Hadley cell and an intensified subtropical jet which both extend significantly polewards than in the modern (July-September). Deposition of the Kimmeridge Clay Formation [KCF] occurred in the shallow, storm-dominated, epeiric Boreal Seaway. High resolution paleo-environmental proxy data from the Kimmeridge Clay Formation [KCF; ~155–150 Ma], UK are used to test for the role of tropical atmospheric circulation on meter-scale heterogeneities in black shale deposition. Proxy and model data show that the most organic-rich section [eudoxus to mid-hudlestoni zones] is characterised by a positive δ13Corg excursion and up to 37 wt% total organic carbon [%TOC]. Orbital-modulation of organic carbon burial primarily in the long eccentricity power band combined with a clear positive correlation between %TOC carbonate-free and the kaolinite/illite ratio supports peak organic carbon burial under the influence of very humid climate conditions, similar to the modern tropics. This re-interpretation of large-scale climate relationships, supported by independent modelling and geological data, has profound implications for atmospheric circulation patterns and processes affecting marine productivity and organic carbon burial further north along the Boreal Seaway, including the Arctic

Cardiovascular Health in Anxiety or Mood Problems Study (CHAMPS): study protocol for a randomized controlled trial

Background: Previous psychological and pharmacological interventions have primarily focused on depression disorders in populations with cardiovascular diseases (CVDs) and the efficacy of anxiety disorder interventions is only more recently being explored. Transdiagnostic interventions address common emotional processes and the full range of anxiety and depression disorders often observed in populations with CVDs. The aim of CHAMPS is to evaluate the feasibility of a unified protocol (UP) for the transdiagnostic treatment of emotional disorders intervention in patients recently hospitalized for CVDs. The current study reports the protocol of a feasibility randomized controlled trial to inform a future trial. Methods/Design: This is a feasibility randomized, controlled trial with a single-center design. A total of 50 participants will be block-randomized to either a UP intervention or enhanced usual care. Both groups will receive standard CVD care. The UP intervention consists of 1) enhancing motivation, readiness for change, and treatment engagement; (2) psychoeducation about emotions; (3) increasing present focused emotion awareness; (4) increasing cognitive flexibility; (5) identifying and preventing patterns of emotion avoidance and maladaptive emotion-driven behaviors (EDBs, including tobacco smoking, and alcohol use); (6) increasing tolerance of emotion-related physical sensations; (7) interoceptive and situation-based emotion-focused exposure; and (8) relapse prevention strategies. Treatment duration is 12 to 18 weeks. Relevant outcomes include the standard deviation of self-rated anxiety, depression and quality of life symptoms. Other outcomes include intervention acceptability, satisfaction with care, rates of EDBs, patient adherence, physical activity, cardiac and psychiatric readmissions. Parallel to the main trial, a nonrandomized comparator cohort will be recruited comprising 150 persons scoring below the predetermined depression and anxiety severity thresholds. Discussion: CHAMPS is designed to evaluate the UP for the transdiagnostic treatment of emotional disorders targeting emotional disorder processes in a CVD population. The design will provide preliminary evidence of feasibility, attrition, and satisfaction with treatment to design a definitive trial. If the trial is feasible, it opens up the possibility for interventions to target broader emotional processes in the precarious population with CVD and emotional distress.Phillip J. Tully, Deborah A. Turnbull, John D. Horowitz, John F. Beltrame, Terina Selkow, Bernhard T. Baune, Elizabeth Markwick, Shannon Sauer-Zavala, Harald Baumeister, Suzanne Cosh and Gary A. Witter

Accurate Prediction of Amide Exchange in the Fast Limit Reveals Thrombin Allostery

Amide hydrogen/deuterium exchange mass spectrometry (HDXMS) of proteins has become extremely popular for identifying ligand-binding sites, protein-protein interactions, intrinsic disorder, and allosteric changes upon protein modification. Such phenomena are revealed when amide exchange is measured in the fast limit, that is, within a few minutes of exchange in deuterated buffer. The HDXMS data have a resolution of the length of peptides and are difficult to interpret because many different phenomena lead to changes in hydrogen/deuterium exchange. We present a quantitative analysis of accelerated molecular dynamics simulations that provides impressive agreement with peptide-length HDXMS data. Comparative analysis of thrombin and a single-point mutant reveals that the simulation analysis can distinguish the subtle differences in exchange due to mutation. In addition, the results provide a deeper understanding of the underlying changes in dynamics revealed by the HDXMS that extend far from the site of mutation

Correlated motions and residual frustration in thrombin.

Thrombin is the central protease in the cascade of blood coagulation proteases. The structure of thrombin consists of a double β-barrel core surrounded by connecting loops and helices. Compared to chymotrypsin, thrombin has more extended loops that are thought to have arisen from insertions in the serine protease that evolved to impart greater specificity. Previous experiments showed thermodynamic coupling between ligand binding at the active site and distal exosites. We present a combined approach of molecular dynamics (MD), accelerated molecular dynamics (AMD), and analysis of the residual local frustration of apo-thrombin and active-site-bound (PPACK-thrombin). Community analysis of the MD ensembles identified changes upon active site occupation in groups of residues linked through correlated motions and physical contacts. AMD simulations, calibrated on measured residual dipolar couplings, reveal that upon active site ligation, correlated loop motions are quenched, but new ones connecting the active site with distal sites where allosteric regulators bind emerge. Residual local frustration analysis reveals a striking correlation between frustrated contacts and regions undergoing slow time scale dynamics. The results elucidate a motional network that probably evolved through retention of frustrated contacts to provide facile conversion between ensembles of states

Enhanced conformational space sampling improves the prediction of chemical shifts in proteins.

A biased-potential molecular dynamics simulation method, accelerated molecular dynamics (AMD), was combined with the chemical shift prediction algorithm SHIFTX to calculate (1)H(N), (15)N, (13)Calpha, (13)Cbeta, and (13)C' chemical shifts of the ankyrin repeat protein IkappaBalpha (residues 67-206), the primary inhibitor of nuclear factor kappa-B (NF-kappaB). Free-energy-weighted molecular ensembles were generated over a range of acceleration levels, affording systematic enhancement of the conformational space sampling of the protein. We have found that the predicted chemical shifts, particularly for the (15)N, (13)Calpha, and (13)Cbeta nuclei, improve substantially with enhanced conformational space sampling up to an optimal acceleration level. Significant improvement in the predicted chemical shift data coincides with those regions of the protein that exhibit backbone dynamics on longer time scales. Interestingly, the optimal acceleration level for reproduction of the chemical shift data has previously been shown to best reproduce the experimental residual dipolar coupling (RDC) data for this system, as both chemical shift data and RDCs report on an ensemble and time average in the millisecond range