Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 4 de 4
Filtrar
Mais filtros

Base de dados
Tipo de documento
Intervalo de ano de publicação
1.
J Comput Aided Mol Des ; 31(7): 609-624, 2017 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-28573346

RESUMO

Finite element (FE) modeling approach has emerged as an efficient way of calculating the dynamic properties of supramolecular protein structures and their complexes. Its efficiency mainly stems from the fact that the complexity of three-dimensional shape of a molecular surface dominates the computational cost rather than the molecular size or the number of atoms. However, no critical evaluation of the method has been made yet particularly for its sensitivity to the parameters used in model construction. Here, we make a close investigation on the effect of FE model parameters by analyzing 135 representative protein structures whose normal modes calculated using all-atom normal mode analysis are publicly accessible online. Results demonstrate that it is more beneficial to use a contour surface of electron densities as the molecular surface, in general, rather than to employ a solvent excluded surface, and that the solution accuracy is almost insensitive to the model parameters unless we avoid extreme values leading to an inaccurate depiction of the characteristic shapes.


Assuntos
Análise de Elementos Finitos , Proteínas/química , Algoritmos , Cinética , Modelos Moleculares , Conformação Proteica , Solventes , Propriedades de Superfície
2.
ACS Nano ; 15(1): 1002-1015, 2021 01 26.
Artigo em Inglês | MEDLINE | ID: mdl-33410664

RESUMO

Structural DNA nanotechnology plays an ever-increasing role in advanced biomolecular applications. Here, we present a computational method to analyze structured DNA assemblies rapidly at near-atomic resolution. Both high computational efficiency and molecular-level accuracy are achieved by developing a multiscale analysis framework. The sequence-dependent relative geometry and mechanical properties of DNA motifs are characterized by the all-atom molecular dynamics simulation and incorporated into the structural finite element model successfully without significant loss of atomic information. The proposed method can predict the three-dimensional shape, equilibrium dynamic properties, and mechanical rigidities of monomeric to hierarchically assembled DNA structures at near-atomic resolution without adjusting any model parameters. The calculation takes less than only 15 min for most origami-scale DNA nanostructures consisting of 7000-8000 base-pairs. Hence, it is expected to be highly utilized in an iterative design-analysis-revision process for structured DNA assemblies.


Assuntos
DNA , Nanoestruturas , Microscopia de Força Atômica , Simulação de Dinâmica Molecular , Nanotecnologia , Conformação de Ácido Nucleico
3.
Sci Adv ; 4(3): eaao7051, 2018 03.
Artigo em Inglês | MEDLINE | ID: mdl-29682606

RESUMO

We mundanely observe cellulose (kitchen) sponges swell while absorbing water. Fluid flows in deformable porous media, such as soils and hydrogels, are classically described on the basis of the theories of Darcy and poroelasticity, where the expansion of media arises due to increased pore pressure. However, the situation is qualitatively different in cellulosic porous materials like sponges because the pore expansion is driven by wetting of the surrounding cellulose walls rather than by increase of the internal pore pressure. We address a seemingly so simple but hitherto unanswered question of how fast water wicks into the swelling sponge. Our experiments uncover a power law of the wicking height versus time distinct from that for nonswelling materials. The observation using environmental scanning electron microscopy reveals the coalescence of microscale wall pores with wetting, which allows us to build a mathematical model for pore size evolution and the consequent wicking dynamics. Our study sheds light on the physics of water absorption in hygroscopically responsive multiscale porous materials, which have far more implications than everyday activities (for example, cleaning, writing, and painting) carried out with cellulosic materials (paper and sponge), including absorbent hygiene products, biomedical cell cultures, building safety, and cooking.

4.
J Chem Theory Comput ; 11(9): 4260-72, 2015 Sep 08.
Artigo em Inglês | MEDLINE | ID: mdl-26575921

RESUMO

Despite recent advances in molecular simulation technologies, analysis of high-molecular-weight structures is still challenging. Here, we propose an automated model reduction procedure aiming to enable modular analysis of these structures. It employs a component mode synthesis for the reduction of finite element protein models. Reduced models may consist of real biological subunits or artificial partitions whose dynamics is described using the degrees of freedom at the substructural interfaces and a small set of dominant vibrational modes only. Notably, the proper number of dominant modes is automatically determined using a novel estimator for eigenvalue errors without calculating the reference eigensolutions of the full model. The performance of the proposed approach is thoroughly investigated by analyzing 50 representative structures including a crystal structure of GroEL and an electron density map of a ribosome.


Assuntos
Chaperonina 60/química , Ribossomos/química , Elétrons , Escherichia coli/química , Modelos Moleculares , Conformação Proteica , Vibração
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA