اشترك بالحزمة الذهبية واحصل على وصول غير محدود شمرا أكاديميا
تسجيل مستخدم جديدThe cardiac Ca-sensitive regulatory switch, a system in dynamic equilibrium
136
0
0.0
(
0
)
اسأل ChatGPT حول البحث
ﻻ يوجد ملخص باللغة العربية
The Ca-sensitive regulatory switch of cardiac muscle is a paradigmatic example of protein assemblies that communicate ligand binding through allosteric change. The switch is a dimeric complex of troponin C (TnC), an allosteric sensor for Ca, and troponin I (TnI), an allosteric reporter. Time-resolved equilibrium FRET measurements suggest that the switch activates in two steps: a TnI-independent Ca-priming step followed by TnI-dependent opening. To resolve the mechanistic role of TnI in activation we performed stopped-flow FRET measurements of activation following rapid addition of a lacking component (Ca or TnI) and deactivation following rapid chelation of Ca. The time-resolved measurements, stopped-flow measurements, and Ca-titration measurements were globally analyzed in terms of a new quantitative dynamic model of TnC-TnI allostery. The analysis provided a mesoscopic parameterization of distance changes, free energy changes, and transition rates among the accessible coarse-grained states of the system. The results reveal (i) the Ca-induced priming step, which precedes opening, is the rate limiting step in activation, (ii) closing is the rate limiting step in deactivation, (iii) TnI induces opening, (iv) an incompletely deactivated population when regulatory Ca is not bound, which generates an accessory pathway of activation, and (v) incomplete activation by Ca--when regulatory Ca is bound, a 3:2 mixture of dynamically inter-converting open (active) and primed-closed (partially active) conformers is observed (15 C). Temperature-dependent stopped-flow FRET experiments provide a near complete thermo-kinetic parametrization of opening. <Abstract Truncated>
قيم البحث
اقرأ أيضاً
The Na$^+$/K$^+$ ATPase is an essential component of cardiac electrophysiology, maintaining physiological Na$^+$ and K$^+$ concentrations over successive heart beats. Terkildsen et al. (2007) developed a model of the ventricular myocyte Na$^+$/K$^+$
ATPase to study extracellular potassium accumulation during ischaemia, demonstrating the ability to recapitulate a wide range of experimental data, but unfortunately there was no archived code associated with the original manuscript. Here we detail an updated version of the model and provide CellML and MATLAB code to ensure reproducibility and reusability. We note some errors within the original formulation which have been corrected to ensure that the model is thermodynamically consistent, and although this required some reparameterisation, the resulting model still provides a good fit to experimental measurements that demonstrate the dependence of Na$^+$/K$^+$ ATPase pumping rate upon membrane voltage and metabolite concentrations. To demonstrate thermodynamic consistency we also developed a bond graph version of the model. We hope that these models will be useful for community efforts to assemble a whole-cell cardiomyocyte model which facilitates the investigation of cellular energetics.
Equilibrium sampling of biomolecules remains an unmet challenge after more than 30 years of atomistic simulation. Efforts to enhance sampling capability, which are reviewed here, range from the development of new algorithms to parallelization to nove
l uses of hardware. Special focus is placed on classifying algorithms -- most of which are underpinned by a few key ideas -- in order to understand their fundamental strengths and limitations. Although algorithms have proliferated, progress resulting from novel hardware use appears to be more clear-cut than from algorithms alone, partly due to the lack of widely used sampling measures.
SARS-CoV-2 is what has caused the COVID-19 pandemic. Early viral infection is mediated by the SARS-CoV-2 homo-trimeric Spike (S) protein with its receptor binding domains (RBDs) in the receptor-accessible state. We performed molecular dynamics simula
tion on the S protein with a focus on the function of its N-terminal domains (NTDs). Our study reveals that the NTD acts as a wedge and plays a crucial regulatory role in the conformational changes of the S protein. The complete RBD structural transition is allowed only when the neighboring NTD that typically prohibits the RBDs movements as a wedge detaches and swings away. Based on this NTD wedge model, we propose that the NTD-RBD interface should be a potential drug target.
We study a protein-DNA target search model with explicit DNA dynamics applicable to in vitro experiments. We show that the DNA dynamics plays a crucial role for the effectiveness of protein jumps between sites distant along the DNA contour but close
in 3D space. A strongly binding protein that searches by 1D sliding and jumping alone, explores the search space less redundantly when the DNA dynamics is fast on the timescale of protein jumps than in the opposite frozen DNA limit. We characterize the crossover between these limits using simulations and scaling theory. We also rationalize the slow exploration in the frozen limit as a subtle interplay between long jumps and long trapping times of the protein in islands within random DNA configurations in solution.
Test experiments of hybridization in DNA microarrays show systematic deviations from the equilibrium isotherms. We argue that these deviations are due to the presence of a partially hybridized long-lived state, which we include in a kinetic model. Ex
periments confirm the model predictions for the intensity vs. free energy behavior. The existence of slow relaxation phenomena has important consequences for the specificity of microarrays as devices for the detection of a target sequence from a complex mixture of nucleic acids.
سجل دخول لتتمكن من نشر تعليقات
التعليقات
جاري جلب التعليقات
سجل دخول لتتمكن من متابعة معايير البحث التي قمت باختيارها
