Insights into the Cooperative Nature of ATP Hydrolysis in Actin Filaments

Abstract

Actin filaments continually assemble and disassemble within a cell. Assembled filaments ''age'' as a bound nucleotide ATP within each actin subunit quickly hydrolyzes followed by a slower release of the phosphate P i , leaving behind a bound ADP. This subtle change in nucleotide state of actin subunits affects filament rigidity as well as its interactions with binding partners. We present here a systematic multiscale ultra-coarse-graining approach that provides a computationally efficient way to simulate a long actin filament undergoing ATP hydrolysis and phosphate-release reactions while systematically taking into account available atomistic details. The slower conformational changes and their dependence on the chemical reactions are simulated with the ultra-coarse-graining model by assigning internal states to the coarse-grained sites. Each state is represented by a unique potential surface of a local heterogeneous elastic network. Internal states undergo stochastic transitions that are coupled to conformations of the underlying molecular system. The model reproduces mechanical properties of the filament and allows us to study whether conformational fluctuations in actin subunits produce cooperative filament aging. We find that the nucleotide states of neighboring subunits modulate the reaction kinetics, implying cooperativity in ATP hydrolysis and P i release. We further systematically coarse grain the system into a Markov state model that incorporates assembly and disassembly, facilitating a direct comparison with previously published models. We find that cooperativity in ATP hydrolysis and P i release significantly affects the filament growth dynamics only near the critical G-actin concentration, whereas far from it, both cooperative and random mechanisms show similar growth dynamics. In contrast, filament composition in terms of the bound nucleotide distribution varies significantly at all monomer concentrations studied. These results provide new insights, to our knowledge, into the cooperative nature of ATP hydrolysis and P i release and the implications it has for actin filament properties, providing novel predictions for future experimental studies.

Nampt-mediated spindle sizing secures a post-anaphase increase in spindle speed required for extreme asymmetry

“…The foregoing showed that either depletion or inhibition of Nampt reduced the levels of both NAD and ATP in oocytes. Due to the key role of the actin cytoskeleton in asymmetric division and the importance of ATP and Nampt-dependent NAD for actin regulation [22][23][24] , we therefore investigated whether altered F-actin behaviour might contribute to defective asymmetry following Nampt-depletion. Cytoplasmic F-actin polymerisation undergoes a marked increase at the time of anaphase-onset in oocytes detectable using a fluorescent utrophin probe (UtrCH-mCherry) 2,7,25,26 .…”

“…Moreover, disruption of kinesin family members including Kif4 41 , HSET (a kinesin-14) 42 and Kif17 43 increase spindle length and in the case of Kif4 44 and Kif17 43 , lead to enlarged first PBs. The actin cytoskeleton, which mediates spindle movement in oocytes 1,7 , is also heavily dependent upon ATP availability [22][23][24]45 . However, our work did not identify any alterations in either cortical or cytoplasmic F-actin behaviour following Nampt-depletion, although it remains possible that another actin-dependent process may be involved.…”

A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion

“…The proteolytic cleavage of the spike and large-scaleconformational shift towards fusion peptide insertion, however, are more difficult to sample in atomistic simulations. To address these issues, one can use CG molecular simulation techniques that allow CG particles to adaptively switch discrete "states" and interactions, such as "Ultra-Coarse-Graining" (UCG)(57)(58)(59). In the limit of infrequent internal state switches, UCG implements microscopically reversible state changes are coupled to a Metropolis Hastings like criterion:…”

Multiscale simulation of actin filaments and actin-associated proteins

“…Such models reduce large-scale complex process into simpler phenomenology, but typically have somewhat limited predictive power and can potentially lack a rigorous justification for the choice of parameters involved. On the other hand, Bbottom-up^CG models of actin filaments with a CG force-field parameterized using reference AA simulations, such as the hetero-elastic network model (hENM), have been found to be adequate in studying actin filaments in terms of their structure and mechanical properties (Chu and Voth 2005;Chu and Voth 2006;Deriu et al 2011;Katkar et al 2018;Lyman et al 2008;Saunders and Voth 2012b;Schramm et al 2017;Voth 2017;Zhang et al 2008). We limit this review below to such bottom-up CG models.…”

“…d Intuitive 12-sitesper-subunit CG model of actin, shown in a subunit and a section of the filament. e Cooperativity in phosphate release rate (reproduced from Katkar et al (2018)) et Fan et al 2012;Hocky et al 2016;Lyman et al 2008;Pfaendtner et al 2010a;Pfaendtner et al 2010b;Pfaendtner et al 2012;Saunders and Voth 2012a;Saunders and Voth 2012b;Schramm et al 2017;Yogurtcu et al 2012) and properties of the single subunit (Chu and Voth 2005;Mehrafrooz and Shamloo 2018;Pfaendtner et al 2009;Saunders et al 2014;Saunders and Voth 2011) to the hydrolysis of the bound nucleotide (Akola and Jones 2006;Freedman et al 2012;McCullagh et al 2014;Sun et al 2017). At the highest resolution, ab initio molecular dynamics (AIMD), density functional theory, or quantum mechanics/ molecular mechanics (QM/MM) simulations allow one to simulate the reactive nature of chemical bonds in ATP and surrounding species using electronic structure theory and the rest of the system using molecular mechanics to make the simulations computationally more efficient.…”