Self-assembly of artificial microtubules

Cheng, Shengfeng; Aggarwal, Ankush; Stevens, Mark J.

doi:10.1039/c2sm25068c

Cited by 32 publications

(41 citation statements)

References 54 publications

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“…Mobile ions are sometimes included explicitly for additional realism, some of the CG water models have specific ion parameters . Very often, even less detailed representations of the solvent are employed, where all of the solvent effects are essentially parameterized into the existing pairwise bead–bead interactions, without a separate solvation term in the Hamiltonian.…”

Section: Coarse‐grained Water Modelsmentioning

confidence: 99%

Water models for biomolecular simulations

Onufriev

Izadi²

2017

WIREs Comput Mol Sci

176

225

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Modern simulation and modeling approaches to investigation of biomolecular structure and function rely heavily on a variety of methods—water models—to approximate the influence of solvent. We give a brief overview of several distinct classes of available water models, with the emphasis on the conceptual basis at each level of approximation. The main focus is on classes of models most widely used in atomistic simulations, including popular implicit and explicit solvent models. Among the latter, nonpolarizable N‐point models are covered in most detail, including some recent methodological advances and nuances. Notes on practical availability and usage in biomolecular simulations are included. Atomistic simulations that were hardly possible only a short while ago have revealed significant problems that can be traced to deficiencies of most commonly used N‐point water models. Recently developed models of this class approximate experimental properties of liquid water much closer than before, and show promise in practical biomolecular simulations. Obstacles to wider adoption of these more accurate water models, both technical and conceptual, are discussed. It is argued that verifying robustness of simulation results to the choice of water model can be of immediate benefit even in the absence of a clear replacement for older models; a specific strategy is proposed. The review is concluded with a discussion on how force‐field development efforts can benefit from better solvent models, and vice versa. WIREs Comput Mol Sci 2018, 8:e1347. doi: 10.1002/wcms.1347 This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics Molecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo Methods

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Section: Coarse‐grained Water Modelsmentioning

confidence: 99%

Water models for biomolecular simulations

Onufriev

Izadi²

2017

WIREs Comput Mol Sci

176

225

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“…One surprise found in our previous simulations using the achiral M 0 is the preferential assembly of helical tubules with pitch 1 or even 2. [22] New results here show that tubules with pitch mismatching the monomer chirality still assemble even for chiral monomers. We found that one factor that can help suppress the mismatch and better control the tubule pitch is to make vertical binding stronger.…”

Section: Simulation Methodsmentioning

confidence: 76%

Self-assembly of chiral tubules

Cheng

Stevens

2014

Soft Matter

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The efficient and controlled assembly of complex structures from macromolecular building blocks is a critical open question in both biological systems and nanoscience. Using molecular dynamics simulations we study the self-assembly of tubular structures from model macromolecular monomers with multiple binding sites on their surfaces [Cheng et al., Soft Matter, 2012, 8, 5666-5678]. In this work we add chirality to the model monomer and a lock-and-key interaction. The self-assembly of free monomers into tubules yields a pitch value that often does not match the chirality of the monomer (including achiral monomers). We show that this mismatch occurs because of a twist deformation that brings the lateral interaction sites into alignment when the tubule pitch differs from the monomer chirality. The energy cost for this deformation is small as the energy distributions substantially overlap for small differences in the pitch and chirality. In order to control the tubule pitch by preventing the twist deformation, the interaction between the vertical surfaces must be increased without resulting in kinetically trapped structures. For this purpose, we employ lock-and-key interactions and obtain good control of the self-assembled tubule pitch. These results explain some fundamental features of microtubules. The vertical interaction strength is larger than the lateral in microtubules because this yields a controlled assembly of tubules with the proper pitch. We also generally find that the control of the assembly into tubules is difficult, which explains the wide range of pitch values and protofilament numbers observed in microtubule assembly.

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“…For example, molecular dynamics (MD) simulations using a wedge‐shaped monomer (Fig. a) have recently demonstrated that self‐assembly into tubule structures depends on key factors such as molecular orientation and the relative influences of both lateral (transverse to the tube) and vertical (along the tube length) molecular interaction strengths (Cheng et al, ; Cheng and Stevens ). MD has further shown that the pitch of the tubule can be controlled by the chirality of the monomer, but also that a twist deformation tends to yield a range of pitch values.…”

Section: Toward Artificial Microtubule Filamentsmentioning

confidence: 99%

Microtubule‐based nanomaterials: Exploiting nature's dynamic biopolymers

Bachand

Spoerke

Stevens

2015

Biotech & Bioengineering

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For more than a decade now, biomolecular systems have served as an inspiration for the development of synthetic nanomaterials and systems that are capable of reproducing many of unique and emergent behaviors of living systems. One intriguing element of such systems may be found in a specialized class of proteins known as biomolecular motors that are capable of performing useful work across multiple length scales through the efficient conversion of chemical energy. Microtubule (MT) filaments may be considered within this context as their dynamic assembly and disassembly dissipate energy, and perform work within the cell. MTs are one of three cytoskeletal filaments in eukaryotic cells, and play critical roles in a range of cellular processes including mitosis and vesicular trafficking. Based on their function, physical attributes, and unique dynamics, MTs also serve as a powerful archetype of a supramolecular filament that underlies and drives multiscale emergent behaviors. In this review, we briefly summarize recent efforts to generate hybrid and composite nanomaterials using MTs as biomolecular scaffolds, as well as computational and synthetic approaches to develop synthetic one-dimensional nanostructures that display the enviable attributes of the natural filaments.

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Self-assembly of artificial microtubules

Cited by 32 publications

References 54 publications

Water models for biomolecular simulations

Water models for biomolecular simulations

Self-assembly of chiral tubules

Microtubule‐based nanomaterials: Exploiting nature's dynamic biopolymers

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