scholarly journals Structure, Dynamics, and Interactions of GPI-Anchored Human Glypican-1 with Heparan Sulfates in a Membrane

Glycobiology ◽  
2020 ◽  
Author(s):  
Chuqiao Dong ◽  
Yeol Kyo Choi ◽  
Jumin Lee ◽  
X Frank Zhang ◽  
Aurelia Honerkamp-Smith ◽  
...  
Keyword(s):  
Molecular Modeling ◽  
Modeling And Simulation ◽  
Degrees Of Freedom ◽  
Membrane Surface ◽  
Structural Features ◽  
Growth Factor Signaling ◽  
Gpi Anchor ◽  
Structure Dynamics ◽  
Heparan Sulfates ◽  
High Flexibility

Abstract Glypican-1 and its heparan sulfate (HS) chains play important roles in modulating many biological processes including growth factor signaling. Glypican-1 is bound to a membrane surface via a glycosylphosphatidylinositol (GPI)-anchor. In this study, we used all-atom molecular modeling and simulation to explore the structure, dynamics, and interactions of GPI-anchored glypican-1, three HS chains, membranes, and ions. The folded glypican-1 core structure is stable, but has substantial degrees of freedom in terms of movement and orientation with respect to the membrane due to the long unstructured C-terminal region linking the core to the GPI-anchor. With unique structural features depending on the extent of sulfation, high flexibility of HS chains can promote multi-site interactions with surrounding molecules near and above the membrane. This study is a first step toward all-atom molecular modeling and simulation of the glycocalyx, as well as its modulation of interactions between growth factors and their receptors.

Ultrastructural identification of three types of sensory setae on copepod antennae

1995 ◽  
Vol 53 ◽  
pp. 956-957
Author(s):  
T. M. Weatherby ◽  
P.H. Lenz
Keyword(s):  
Phase Locking ◽  
Membrane Surface ◽  
Reaction Times ◽  
High Sensitivity ◽  
Structural Features ◽  
Calanoid Copepods ◽  
Marine Food Webs ◽  
Dendritic Membrane ◽  
Ultrastructural Characterization

Crustaceans, as well as other arthropods, are covered with sensory setae and hairs, including mechanoand chemosensory sensillae with a ciliary origin. Calanoid copepods are small planktonic crustaceans forming a major link in marine food webs. In conjunction with behavioral and physiological studies of the antennae of calanoids, we undertook the ultrastructural characterization of sensory setae on the antennae of Pleuromamma xiphias.Distal mechanoreceptive setae exhibit exceptional behavioral and physiological performance characteristics: high sensitivity (<10 nm displacements), fast reaction times (<1 msec latency) and phase locking to high frequencies (1-2 kHz). Unusual structural features of the mechanoreceptors are likely to be related to their physiological sensitivity. These features include a large number (up to 3000) of microtubules in each sensory cell dendrite, arising from or anchored to electron dense rods associated with the ciliary basal body microtubule doublets. The microtubules are arranged in a regular array, with bridges between and within rows. These bundles of microtubules extend far into each mechanoreceptive seta and terminate in a staggered fashion along the dendritic membrane, contacting a large membrane surface area and providing a large potential site of mechanotransduction.

scholarly journals Three-Dimensional Structures of Carbohydrates and Where to Find Them

2020 ◽  
Vol 21 (20) ◽  
pp. 7702 ◽  
Author(s):  
Sofya I. Scherbinina ◽  
Philip V. Toukach
Keyword(s):  
Experimental Data ◽  
Molecular Modeling ◽  
Computational Methods ◽  
Three Dimensional ◽  
Structural Diversity ◽  
Structural Data ◽  
Structural Features ◽  
Data Validation ◽  
Data Generation ◽  
Efficient Treatment

Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.

scholarly journals Computational Molecular Modeling of Transport Processes in Nanoporous Membranes

Processes ◽  
2018 ◽  
Vol 6 (8) ◽  
pp. 124 ◽  
Author(s):  
Kevin Hinkle ◽  
Xiaoyu Wang ◽  
Xuehong Gu ◽  
Cynthia Jameson ◽  
Sohail Murad
Keyword(s):  
Molecular Modeling ◽  
Temporal Resolution ◽  
High Performance ◽  
Low Cost ◽  
Membrane Surface ◽  
Experimental Studies ◽  
Nanoporous Materials ◽  
Transport Processes ◽  
Zeolite Membrane ◽  
Nanoporous Membranes

In this report we have discussed the important role of molecular modeling, especially the use of the molecular dynamics method, in investigating transport processes in nanoporous materials such as membranes. With the availability of high performance computers, molecular modeling can now be used to study rather complex systems at a fraction of the cost or time requirements of experimental studies. Molecular modeling techniques have the advantage of being able to access spatial and temporal resolution which are difficult to reach in experimental studies. For example, sub-Angstrom level spatial resolution is very accessible as is sub-femtosecond temporal resolution. Due to these advantages, simulation can play two important roles: Firstly because of the increased spatial and temporal resolution, it can help understand phenomena not well understood. As an example, we discuss the study of reverse osmosis processes. Before simulations were used it was thought the separation of water from salt was purely a coulombic phenomenon. However, by applying molecular simulation techniques, it was clearly demonstrated that the solvation of ions made the separation in effect a steric separation and it was the flux which was strongly affected by the coulombic interactions between water and the membrane surface. Additionally, because of their relatively low cost and quick turnaround (by using multiple processor systems now increasingly available) simulations can be a useful screening tool to identify membranes for a potential application. To this end, we have described our studies in determining the most suitable zeolite membrane for redox flow battery applications. As computing facilities become more widely available and new computational methods are developed, we believe molecular modeling will become a key tool in the study of transport processes in nanoporous materials.

The Research and Simulation Analysis of a New Type of Translational Transmission Device

2014 ◽  
Vol 556-562 ◽  
pp. 1408-1412
Author(s):  
Zhi Qiang Zhang
Keyword(s):  
Modeling And Simulation ◽  
Theoretical Foundation ◽  
Simulation Analysis ◽  
Structural Modeling ◽  
Structural Features ◽  
Practical Application ◽  
Optimization Analysis ◽  
New Type ◽  
Mechanism Parameter ◽  
Relationship Of

In this paper, the following work is done: a new type of translational transmission device is designed; explained in detail are the operating principle, structural features, relationship of mechanism parameter and non interference conditions of the movement; the optimization analysis of transmission device is implemented on the basis of non interference conditions of the bucket movement; structural modeling and simulation analysis are carried out by utilization of Pro/e & Recurdyn; and based on virtual prototype technology, the new type of translational transmission device is verified by experiments, the data of which prove the translational transmission device reasonable and practicable. In conclusion, this paper has laid the theoretical foundation of the practical application of the translational transmission device.

Molecular modeling and simulation analysis of glaucoma pathway

2016 ◽  
Vol 5 (1) ◽  
Author(s):  
Jyoti Kant Choudhari ◽  
Jyotsna Choubey ◽  
Ashish Patel ◽  
Mukesh Kumar Verma
Keyword(s):  
Molecular Modeling ◽  
Modeling And Simulation ◽  
Simulation Analysis

scholarly journals "Dividing and Conquering" and "Caching" in Molecular Modeling

2021 ◽  
Author(s):  
Xiaoyong Cao ◽  
Pu Tian
Keyword(s):  
Molecular Modeling ◽  
Degrees Of Freedom ◽  
Materials Science ◽  
Force Fields ◽  
Coarse Graining ◽  
Divide And Conquer ◽  
Collective Variables ◽  
Molecular Systems ◽  
State Models ◽  
Molecular Science

Molecular modeling is widely utilized in subjects including but not limited to physics, chemistry, biology, materials science and engineering. Impressive progress has been made in development of theories, algorithms and software packages. To divide and conquer, and to cache intermediate results have been long standing principles in development of algorithms. Not surprisingly, Most of important methodological advancements in more than half century of molecule modeling are various implementations of these two fundamental principles. In the mainstream classical computational molecular science based on force fields parameterization by coarse graining, tremendous efforts have been invested on two lines of algorithm development. The first is coarse graining, which is to represent multiple basic particles in higher resolution modeling as a single larger and softer particle in lower resolution counterpart, with resulting force fields of partial transferability at the expense of some information loss. The second is enhanced sampling, which realizes "dividing and conquering" and/or "caching" in configurational space with focus either on reaction coordinates and collective variables as in metadynamics and related algorithms, or on the transition matrix and state discretization as in Markov state models. For this line of algorithms, spatial resolution is maintained but no transferability is available. Deep learning has been utilized to realize more efficient and accurate ways of "dividing and conquering" and "caching" along these two lines of algorithmic research. We proposed and demonstrated the local free energy landscape approach, a new framework for classical computational molecular science and a third class of algorithm that facilitates molecular modeling through partially transferable in resolution "caching" of distributions for local clusters of molecular degrees of freedom. Differences, connections and potential interactions among these three algorithmic directions are discussed, with the hope to stimulate development of more elegant, efficient and reliable formulations and algorithms for "dividing and conquering" and "caching" in complex molecular systems.

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