Brownian Ratchets Driven by Asymmetric Nucleation of Hydrolysis Waves

Lakhanpal, Amit; Chou, Tom

doi:10.1103/physrevlett.99.248302

Cited by 7 publications

(5 citation statements)

References 13 publications

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“…This solution is similar in spirit to Kittel's single-ended zipper model for DNA [24]. Asymmetric cooperativity has also been proposed earlier to explain other biophysical processes [25]. Such an arrangement would prolong the lifetimes of the already-formed hydrogen bonds to the pair's left, and thus would increase the probability for covalent bonding among those bonded monomers.…”

Section: The Modelsupporting

confidence: 67%

Evolutionary advantage of directional symmetry breaking in self-replicating polymers

Subramanian

Gatenby

2018

Journal of Theoretical Biology

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Due to the asymmetric nature of the nucleotides, the extant informational biomolecule, DNA, is constrained to replicate unidirectionally on a template. As a product of molecular evolution that sought to maximize replicative potential, DNA's unidirectional replication poses a mystery since symmetric bidirectional self-replicators obviously would replicate faster than unidirectional self-replicators and hence would have been evolutionarily more successful. Here we carefully examine the physico-chemical requirements for evolutionarily successful primordial self-replicators and theoretically show that at low monomer concentrations that possibly prevailed in the primordial oceans, asymmetric unidirectional self-replicators would have an evolutionary advantage over bidirectional self-replicators. The competing requirements of low and high kinetic barriers for formation and long lifetime of inter-strand bonds respectively are simultaneously satisfied through asymmetric kinetic influence of inter-strand bonds, resulting in evolutionarily successful unidirectional self-replicators. Within our model, circular strands, the configuration prefered by primitive life forms, have higher replicative potential compared to linear strands.

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Section: The Modelsupporting

confidence: 67%

Evolutionary advantage of directional symmetry breaking in self-replicating polymers

Subramanian

Gatenby

2018

Journal of Theoretical Biology

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“…This solution is similar in spirit to Kittel's single-ended zipper model for DNA [23]. Asymmetric cooperativity has also been proposed earlier to explain other biophysical processes [24]. Such an arrangement would prolong the lifetimes of the already-formed hydrogen bonds to the pair's left, and thus would increase the probability for covalent bonding among those bonded monomers.…”

Section: The Modelsupporting

confidence: 67%

Evolutionary advantage of a broken symmetry in autocatalytic polymers explains fundamental properties of DNA

Subramanian¹,

Gatenby²

2016

Preprint

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The macromolecules that encode and translate information in living systems, DNA and RNA, exhibit distinctive structural asymmetries, including homochirality or mirror image asymmetry and 3 -5 directionality, that are invariant across all life forms. The evolutionary advantages of these broken symmetries remain unknown. Here we utilize a very simple model of hypothetical self-replicating polymers to show that asymmetric autocatalytic polymers are more successful in self-replication compared to their symmetric counterparts in the Darwinian competition for space and common substrates. This broken-symmetry property, called asymmetric cooperativity, arises with the maximization of a replication potential, where the catalytic influence of inter-strand bonds on their left and right neighbors is unequal. Asymmetric cooperativity also leads to tentative, qualitative and simple evolution-based explanations for a number of other properties of DNA that include four nucleotide alphabet, three nucleotide codons, circular genomes, helicity, anti-parallel double-strand orientation, heteromolecular base-pairing, asymmetric base compositions, and palindromic instability, apart from the structural asymmetries mentioned above. Our model results and tentative explanations are consistent with multiple lines of experimental evidence, which include evidence for the presence of asymmetric cooperativity in DNA.

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“…Several studies have examined track-induced transport (Antal and Krapivsky, 2005;Artyomov et al, 2008;Morozov, 2007;Saffarian et al, 2006). Here, we discuss directed transport of a Holliday junction along DNA (Lakhanpal and Chou, 2007).…”

Section: Local Target Signalingmentioning

confidence: 99%

Stochastic models of intracellular transport

2013

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The interior of a living cell is a crowded, heterogenuous, fluctuating environment. Hence, a major challenge in modeling intracellular transport is to analyze stochastic processes within complex environments. Broadly speaking, there are two basic mechanisms for intracellular transport: passive diffusion and motor-driven active transport. Diffusive transport can be formulated in terms of the motion of an over-damped Brownian particle. On the other hand, active transport requires chemical energy, usually in the form of ATP hydrolysis, and can be direction specific, allowing biomolecules to be transported long distances; this is particularly important in neurons due to their complex geometry. In this review we present a wide range of analytical methods and models of intracellular transport. In the case of diffusive transport, we consider narrow escape problems, diffusion to a small target, confined and single-file diffusion, homogenization theory, and fractional diffusion. In the case of active transport, we consider Brownian ratchets, random walk models, exclusion processes, random intermittent search processes, quasisteady-state reduction methods, and mean field approximations. Applications include receptor trafficking, axonal transport, membrane diffusion, nuclear transport, protein-DNA interactions, virus trafficking, and the self-organization of subcellular structures.

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Brownian Ratchets Driven by Asymmetric Nucleation of Hydrolysis Waves

Cited by 7 publications

References 13 publications

Evolutionary advantage of directional symmetry breaking in self-replicating polymers

Evolutionary advantage of directional symmetry breaking in self-replicating polymers

Evolutionary advantage of a broken symmetry in autocatalytic polymers explains fundamental properties of DNA

Stochastic models of intracellular transport

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