Combining the MARTINI and Structure-Based Coarse-Grained Approaches for the Molecular Dynamics Studies of Conformational Transitions in Proteins

Poma, Adolfo B.; Cieplak, Marek; Theodorakis, Panagiotis E.

doi:10.1021/acs.jctc.6b00986

Cited by 160 publications

(225 citation statements)

References 61 publications

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“…1a), was mapped according to the GoMAR-TINI model, whereas monomers were mapped according to the standard MARTINI model. 25,28 GoMARTINI partially exceeded the main drawback of the MARTINI model allowing us to monitor secondary structure transitions. Indeed, the GoMAR-TINI model has proven to be suitable for the investigation of peptide/protein folding and unfolding processes.…”

Section: Resultsmentioning

confidence: 99%

Probing mechanical properties and failure mechanisms of fibrils of self-assembling peptides

Fontana

Gelain

2020

Nanoscale Adv.

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Self-assembling peptides (SAPs) are a promising class of biomaterials amenable to easy molecular design and functionalization. Despite their increasing usage in regenerative medicine, a detailed analysis of their biomechanics at the nanoscale level is still missing. In this work, we propose and validate, in all-atom dynamics, a coarse-grained model to elucidate strain distribution, failure mechanisms and biomechanical effects of functionalization of two SAPs when subjected to both axial stretching and bending forces. We highlight different failure mechanisms for fibril seeds and fibrils, as well as the negligible contribution of the chosen functional motif to the overall system rupture. This approach could lay the basis for the development of "more" coarse-grained models in the long pathway connecting SAP sequences and hydrogel mechanical properties.

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Section: Resultsmentioning

confidence: 99%

Probing mechanical properties and failure mechanisms of fibrils of self-assembling peptides

Fontana

Gelain

2020

Nanoscale Adv.

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“…In order to reach the necessary time scales to converge to the equilibrium distribution, we use a simplified C α representation of a 17-mer filament and a structure-based model (SBM) [47,44]. Structure-based models (also termed Gō-models) define a known accessible structure as a global energetic minimum and have been shown to capture the slow deformation modes defined by the network of inter-residue interactions [48].…”

Section: Structure-based Coarse-grained Simulationsmentioning

confidence: 99%

Polymer-like model to study the dynamics of dynamin filaments on deformable membrane tubes

Noel

Noé

Daumke

et al. 2019

Preprint

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Peripheral membrane proteins with intrinsic curvature can act both as sensors of membrane curvature and shape modulators of the underlying membranes. A well-studied example of such proteins is the mechano-chemical GTPase dynamin that assembles into helical filaments around membrane tubes and catalyzes their scission in a GTPase-dependent manner. It is known that the dynamin coat alone, without GTP, can constrict membrane tubes to radii of about 10 nanometers, indicating that the intrinsic shape and elasticity of dynamin filaments should play an important role in membrane remodeling. However, molecular and dynamic understanding of the process is lacking. Here, we develop a dynamical polymer-chain model for a helical elastic filament bound on a deformable membrane tube of conserved mass, accounting for thermal fluctuations in the filament and lipid flows in the membrane. The model is based on a locallycylindrical helix approximation for dynamin. We obtain the elastic parameters of the dynamin filament by molecular dynamics simulations of its tetrameric building block and also from coarse-grained structurebased simulations of a 17-dimer filament. The results show that the stiffness of dynamin is comparable to that of the membrane. We determine equilibrium shapes of the filament and the membrane, and find that mostly the pitch of the filament, not its radius, is sensitive to variations in membrane tension and stiffness. The close correspondence between experimental estimates of the inner tube radius and those predicted by the model suggests that dynamin's "stalk" region is responsible for its GTP-independent membraneshaping ability. The model paves the way for future mesoscopic modeling of dynamin with explicit motor function.Understanding the mechanical properties of the dynamin filament is crucial to uncover how it transmits motor force toward the constriction and eventual scission of the underlying membrane template.Dynamin's structure and function in membrane scission have been extensively experimentally studied, as summarized in the detailed review [3]. Although endocytosis involves a complex orchestration of dozens of different proteins [4], it is remarkable that, in the presence of GTP, dynamin alone is sufficient to constrict the membrane, create torque, and perform scission in vitro [5,6]. Through a combination of cryo-electron microscopy [7,8] and X-ray crystallography [9, 10, 11] the structure of the dynamin oligomer on a membrane template has been elucidated ( Fig. 1). Two-fold symmetric dimers of dynamin are formed by a central interface in the stalk. These dimers further assemble into tetramers and polymers through two additional stalk interfaces (the tetramer interface [11]). The resulting stalk filament has an intrinsic helical shape and acts as a scaffold that stabilizes membrane curvature. The pleckstrin homology (PH) domains protrude from the filament toward the membrane and mediate binding to the lipid surface [12,13,14]. Opposite the PH domains are the motor domains which are composed of a GTPase...

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“…proteins), their native structures. 43 To overcome these constraints, coarsegrained (CG) force-fields, that provide adequate resolution for the phenomena involved at the contact line, but at the same time allow access to large time and length scales 44,45 have been developed. SAFT-γ has provided the potential parameters for different components of the CG system including those for water.…”

Section: Molecular Dynamicsmentioning

confidence: 99%

Moving Contact Lines: Linking Molecular Dynamics and Continuum-Scale Modeling

et al. 2018

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Despite decades of research, the modeling of moving contact lines has remained a formidable challenge in fluid dynamics whose resolution will impact numerous industrial, biological, and daily life applications. On the one hand, molecular dynamics (MD) simulation has the ability to provide unique insight into the microscopic details that determine the dynamic behavior of the contact line, which is not possible with either continuum-scale simulations or experiments. On the other hand, continuum-based models provide a link to the macroscopic description of the system. In this Feature Article, we explore the complex range of physical factors, including the presence of surfactants, which governs the contact line motion through MD simulations. We also discuss links between continuum- and molecular-scale modeling and highlight the opportunities for future developments in this area.

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Combining the MARTINI and Structure-Based Coarse-Grained Approaches for the Molecular Dynamics Studies of Conformational Transitions in Proteins

Cited by 160 publications

References 61 publications

Probing mechanical properties and failure mechanisms of fibrils of self-assembling peptides

Probing mechanical properties and failure mechanisms of fibrils of self-assembling peptides

Polymer-like model to study the dynamics of dynamin filaments on deformable membrane tubes

Moving Contact Lines: Linking Molecular Dynamics and Continuum-Scale Modeling

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