Stabilizing Effect of Inherent Knots on Proteins Revealed by Molecular Dynamics Simulations (Q57492549)

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title

Stabilizing Effect of Inherent Knots on Proteins Revealed by Molecular Dynamics Simulations (English)

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28 April 2020

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Yan Xu

1

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Shixin Li

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Zengshuai Yan

3

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Zhen Luo

4

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Hao Ren

5

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Baosheng Ge

6

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Fang Huang

7

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Tongtao Yue

8

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language of work or name

English

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publication date

22 September 2018

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volume

115

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issue

9

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page(s)

1681-1689

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describes a project that uses

28 April 2020

molecular dynamics simulation

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Protein folding in the cell

inferred from title

cites work

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12 December 2020

VMD: visual molecular dynamics

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12 December 2020

The packing density in proteins: standard radii and volumes.

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12 December 2020

A deeply knotted protein structure and how it might fold.

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12 December 2020

Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation

1 reference

12 December 2020

Structure of the YibK methyltransferase from Haemophilus influenzae (HI0766): a cofactor bound at a site formed by a knot

1 reference

12 December 2020

The molecular basis for the chemical denaturation of proteins by urea

1 reference

12 December 2020

Regeneration of enzyme activity by air oxidation of reduced subtilisin-modified ribonuclease

1 reference

12 December 2020

Protein folding and misfolding

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12 December 2020

Theory of protein folding

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12 December 2020

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

1 reference

12 December 2020

Exploring the energy landscape of GFP by single-molecule mechanical experiments

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12 December 2020

A light-sensing knot revealed by the structure of the chromophore-binding domain of phytochrome

1 reference

12 December 2020

Thermal unfolding of proteins

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12 December 2020

Probing nature's knots: the folding pathway of a knotted homodimeric protein

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12 December 2020

Intricate knots in proteins: Function and evolution

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12 December 2020

A backbone-based theory of protein folding

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12 December 2020

A comparison of the folding of two knotted proteins: YbeA and YibK.

1 reference

12 December 2020

Backbone building from quadrilaterals: a fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates

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12 December 2020

The folding mechanics of a knotted protein

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12 December 2020

Protein knots and fold complexity: some new twists.

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12 December 2020

Characterization of the protein unfolding processes induced by urea and temperature

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12 December 2020

Combining experiment and simulation in protein folding: closing the gap for small model systems

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12 December 2020

Tightening of knots in proteins

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12 December 2020

Knotted fusion proteins reveal unexpected possibilities in protein folding

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12 December 2020

Extracting function from a beta-trefoil folding motif

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12 December 2020

Exploring knotting mechanisms in protein folding.

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12 December 2020

Stabilizing effect of knots on proteins

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12 December 2020

How does a knotted protein fold?

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12 December 2020

Dodging the crisis of folding proteins with knots

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12 December 2020

Tightening the knot in phytochrome by single-molecule atomic force microscopy

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12 December 2020

Experimental detection of knotted conformations in denatured proteins

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12 December 2020

Untying knots in proteins.

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12 December 2020

Structure and folding of a designed knotted protein

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12 December 2020

Structures and folding pathways of topologically knotted proteins

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12 December 2020

Simulating water with rigid non-polarizable models: a general perspective

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12 December 2020

Comparison of chemical and thermal protein denaturation by combination of computational and experimental approaches. II.

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12 December 2020

Knot formation in newly translated proteins is spontaneous and accelerated by chaperonins

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12 December 2020

Stretching single polysaccharides and proteins using atomic force microscopy

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12 December 2020

Mechanically untying a protein slipknot: multiple pathways revealed by force spectroscopy and steered molecular dynamics simulations.

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12 December 2020

Conservation of complex knotting and slipknotting patterns in proteins

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12 December 2020

Denaturant-dependent folding of GFP

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12 December 2020

Energy landscape of knotted protein folding

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12 December 2020

Single-molecule detection reveals knot sliding in TrmD denaturation.

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12 December 2020

All-atom empirical potential for molecular modeling and dynamics studies of proteins

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12 December 2020

Mechanically tightening a protein slipknot into a trefoil knot.

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12 December 2020

Mechanistic insights into the folding of knotted proteins in vitro and in vivo

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12 December 2020

KnotProt: a database of proteins with knots and slipknots

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12 December 2020

Molecular dynamics simulations of large macromolecular complexes.

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12 December 2020

Assessment of the utility of contact-based restraints in accelerating the prediction of protein structure using molecular dynamics simulations.

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12 December 2020

Tightening and Untying the Knot in Human Carbonic Anhydrase III.

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12 December 2020

Knotted proteins: A tangled tale of Structural Biology

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12 December 2020

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

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12 December 2020

Knotting and unknotting of a protein in single molecule experiments.

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12 December 2020

In Search of Functional Advantages of Knots in Proteins.

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12 December 2020

Structural entanglements in protein complexes

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12 December 2020

10.1016/J.BPJ.2018.09.015

Identifiers

DOI

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28 April 2020

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28 April 2020

PubMed publication ID

30314655

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