scholarly journals Polymer Nucleation under High-Driving Force, Long-Chain Conditions: Heat Release and the Separation of Timescales

2018 ◽  
Author(s):  
Kyle Hall ◽  
Simona Percec ◽  
Michael Klein
Keyword(s):  
Conformational Changes ◽  
Driving Forces ◽  
Early Stage ◽  
Polymer Crystallization ◽  
Crystal Nucleation ◽  
Crystal Formation ◽  
Polymer Crystal ◽  
Dynamics Simulations ◽  
New Research ◽  
Chain Level

<p>This study reveals two important features of polymer crystal formation at high-driving forces in entangled polymer melts based on molecular dynamics simulations of polyethylene, a prototypical polymer. First, in contrast to existing literature on small-molecule crystallization, it is demonstrated that the heat released during polymer crystallization does not appreciably influence molecular-level structural details of early-stage, crystalline clusters (i.e., polymer crystal nuclei). Second, it is revealed that early-stage polymer crystallization (i.e., crystal nucleation) can occur without substantial chain-level relaxation and conformational changes, which is consistent with previous experimental work and yet in contrast to many previous computational studies. Given the conditions used to process polyethylene, the separation of timescales associated with crystallization and chain-level processes is anticipated to be of substantial importance to processing strategies. This study thus provides insights that highlight new research directions for understanding polymer crystallization under industrially-relevant conditions while also providing guidance as to how this work can be undertaken.</p>

Polymer Nucleation under High-Driving Force, Long-Chain Conditions: Heat Release and the Separation of Timescales

2019 ◽  
Author(s):  
Kyle Hall ◽  
Simona Percec ◽  
Michael Klein
Keyword(s):  
Driving Force ◽  
Polymer Melts ◽  
Early Stage ◽  
Polymer Crystallization ◽  
Crystal Nucleation ◽  
Crystal Formation ◽  
Local Structures ◽  
Entangled Polymer ◽  
Entangled Polymer Melts ◽  
Chain Level

This study reveals important features of polymer crystal formation at high-driving forces in entangled polymer melts based on simulations of polyethylene. First and in contrast to small-molecule crystallization, the heat released during polymer crystallization does not appreciably influence structural details of early-stage, crystalline clusters (crystal nuclei). Second, early-stage polymer crystallization (crystal nucleation) can occur without substantial chain-level relaxation and conformational changes. This study's results indicate that local structures and environments guide crystal nucleation in entangled polymer melts under high-driving force conditions. Given that such conditions are often used to process polyethylene, local structures and the separation of timescales associated with crystallization and chain-level processes are anticipated to be of substantial importance to processing strategies. This study highlights new research directions for understanding polymer crystallization.

Polymer Nucleation under High-Driving Force, Long-Chain Conditions: Heat Release and the Separation of Timescales

2019 ◽  
Author(s):  
Kyle Hall ◽  
Simona Percec ◽  
Michael Klein
Keyword(s):  
Driving Force ◽  
Polymer Melts ◽  
Early Stage ◽  
Polymer Crystallization ◽  
Crystal Nucleation ◽  
Crystal Formation ◽  
Local Structures ◽  
Entangled Polymer ◽  
Entangled Polymer Melts ◽  
Chain Level

This study reveals important features of polymer crystal formation at high-driving forces in entangled polymer melts based on simulations of polyethylene. First and in contrast to small-molecule crystallization, the heat released during polymer crystallization does not appreciably influence structural details of early-stage, crystalline clusters (crystal nuclei). Second, early-stage polymer crystallization (crystal nucleation) can occur without substantial chain-level relaxation and conformational changes. This study's results indicate that local structures and environments guide crystal nucleation in entangled polymer melts under high-driving force conditions. Given that such conditions are often used to process polyethylene, local structures and the separation of timescales associated with crystallization and chain-level processes are anticipated to be of substantial importance to processing strategies. This study highlights new research directions for understanding polymer crystallization.

scholarly journals Early-stage dynamics of chloride ion–pumping rhodopsin revealed by a femtosecond X-ray laser

2021 ◽  
Vol 118 (13) ◽  
pp. e2020486118
Author(s):  
Ji-Hye Yun ◽  
Xuanxuan Li ◽  
Jianing Yue ◽  
Jae-Hyun Park ◽  
Zeyu Jin ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Structural Changes ◽  
Early Stage ◽  
Chloride Ion ◽  
Time Resolved ◽  
X Ray ◽  
Combining Data ◽  
Linac Coherent Light Source ◽  
Dynamics Simulations ◽  
Ion Pumping

Chloride ion–pumping rhodopsin (ClR) in some marine bacteria utilizes light energy to actively transport Cl− into cells. How the ClR initiates the transport is elusive. Here, we show the dynamics of ion transport observed with time-resolved serial femtosecond (fs) crystallography using the Linac Coherent Light Source. X-ray pulses captured structural changes in ClR upon flash illumination with a 550 nm fs-pumping laser. High-resolution structures for five time points (dark to 100 ps after flashing) reveal complex and coordinated dynamics comprising retinal isomerization, water molecule rearrangement, and conformational changes of various residues. Combining data from time-resolved spectroscopy experiments and molecular dynamics simulations, this study reveals that the chloride ion close to the Schiff base undergoes a dissociation–diffusion process upon light-triggered retinal isomerization.

Molecular Basis of Glucose Transport Mechanism in Plants

2019 ◽  
Author(s):  
Balaji Selvam ◽  
Ya-Chi Yu ◽  
Liqing Chen ◽  
Diwakar Shukla
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Conformational Changes ◽  
Transport Mechanism ◽  
Conformational Dynamics ◽  
Site Directed Mutagenesis ◽  
Free Energy Barrier ◽  
Transport Cycle ◽  
Dynamics Simulations

<p>The SWEET family belongs to a class of transporters in plants that undergoes large conformational changes to facilitate transport of sugar molecules across the cell membrane. However, the structures of their functionally relevant conformational states in the transport cycle have not been reported. In this study, we have characterized the conformational dynamics and complete transport cycle of glucose in OsSWEET2b transporter using extensive molecular dynamics simulations. Using Markov state models, we estimated the free energy barrier associated with different states as well as 1 for the glucose the transport mechanism. SWEETs undergoes structural transition to outward-facing (OF), Occluded (OC) and inward-facing (IF) and strongly support alternate access transport mechanism. The glucose diffuses freely from outside to inside the cell without causing major conformational changes which means that the conformations of glucose unbound and bound snapshots are exactly same for OF, OC and IF states. We identified a network of hydrophobic core residues at the center of the transporter that restricts the glucose entry to the cytoplasmic side and act as an intracellular hydrophobic gate. The mechanistic predictions from molecular dynamics simulations are validated using site-directed mutagenesis experiments. Our simulation also revealed hourglass like intermediate states making the pore radius narrower at the center. This work provides new fundamental insights into how substrate-transporter interactions actively change the free energy landscape of the transport cycle to facilitate enhanced transport activity.</p>

scholarly journals Studies of Conformational Changes of Tubulin Induced by Interaction with Kinesin Using Atomistic Molecular Dynamics Simulations

2021 ◽  
Vol 22 (13) ◽  
pp. 6709
Author(s):  
Xiao-Xuan Shi ◽  
Peng-Ye Wang ◽  
Hong Chen ◽  
Ping Xie
Keyword(s):  
Molecular Dynamics ◽  
High Resolution ◽  
Binding Energy ◽  
Molecular Dynamics Simulations ◽  
Conformational Changes ◽  
Weak Interactions ◽  
Molecular Motor ◽  
Structural Data ◽  
Calculated Binding Energy ◽  
Dynamics Simulations

The transition between strong and weak interactions of the kinesin head with the microtubule, which is regulated by the change of the nucleotide state of the head, is indispensable for the processive motion of the kinesin molecular motor on the microtubule. Here, using all-atom molecular dynamics simulations, the interactions between the kinesin head and tubulin are studied on the basis of the available high-resolution structural data. We found that the strong interaction can induce rapid large conformational changes of the tubulin, whereas the weak interaction cannot. Furthermore, we found that the large conformational changes of the tubulin have a significant effect on the interaction of the tubulin with the head in the weak-microtubule-binding ADP state. The calculated binding energy of the ADP-bound head to the tubulin with the large conformational changes is only about half that of the tubulin without the conformational changes.

scholarly journals Advances in the role of miRNAs in the occurrence and development of osteosarcoma

Open Medicine ◽  
2020 ◽  
Vol 15 (1) ◽  
pp. 1003-1011
Author(s):  
Guanyu Zhang ◽  
Yiran Li ◽  
Jiasheng Xu ◽  
Zhenfang Xiong
Keyword(s):  
Target Gene ◽  
Early Stage ◽  
Research Direction ◽  
Research Progress ◽  
Skeletal System ◽  
Translation Process ◽  
Non Coding Rnas ◽  
New Research ◽  
Post Transcriptional Regulation

AbstractOsteosarcoma (OS) is the most common primary malignant tumor of the skeletal system in the clinic. It mainly occurs in adolescent patients and the pathogenesis of the disease is very complicated. The distant metastasis may occur in the early stage, and the prognosis is poor. MicroRNAs (miRNAs) are non-coding RNAs of about 18–25 nt in length that are involved in post-transcriptional regulation of genes. miRNAs can regulate target gene expression by promoting the degradation of target mRNAs or inhibiting the translation process, thereby the proliferation of OS cells can be inhibited and the apoptosis can be promoted; in this way, miRNAs can affect the metabolism of OS cells and can also participate in the occurrence, invasion, metastasis, and recurrence of OS. Some miRNAs have already been found to be closely related to the prognosis of patients with OS. Unlike other reviews, this review summarizes the miRNA molecules closely related to the development, diagnosis, prognosis, and treatment of OS in recent years. The expression and influence of miRNA molecule on OS were discussed in detail, and the related research progress was summarized to provide a new research direction for early diagnosis and treatment of OS.

scholarly journals Molecular Dynamics Simulations of Crystal Nucleation near Interfaces in Incompatible Polymer Blends

Polymers ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 347
Author(s):  
Wenlin Zhang ◽  
Lingyi Zou
Keyword(s):  
Molecular Dynamics ◽  
Polymer Blends ◽  
Md Simulations ◽  
Nucleation And Growth ◽  
Crystal Nucleation ◽  
Crystalline Order ◽  
Mobile Species ◽  
Deep Supercooling ◽  
Crystallizable Polymer ◽  
Dynamics Simulations

We apply molecular dynamics (MD) simulations to investigate crystal nucleation in incompatible polymer blends under deep supercooling conditions. Simulations of isothermal nucleation are performed for phase-separated blends with different degrees of incompatibility. In weakly segregated blends, slow and incompatible chains in crystallizable polymer domains can significantly hinder the crystal nucleation and growth. When a crystallizable polymer is blended with a more mobile species in interfacial regions, enhanced molecular mobility leads to the fast growth of crystalline order. However, the incubation time remains the same as that in pure samples. By inducing anisotropic alignment near the interfaces of strongly segregated blends, phase separation also promotes crystalline order to grow near interfaces between different polymer domains.

Insights into the roles of charged residues in substrate binding and mode of action of mannuronan C-5 epimerase AlgE4

Glycobiology ◽  
2021 ◽  
Author(s):  
Margrethe Gaardløs ◽  
Sergey A Samsonov ◽  
Marit Sletmoen ◽  
Maya Hjørnevik ◽  
Gerd Inger Sætrom ◽  
...  
Keyword(s):  
Optical Tweezers ◽  
Conformational Changes ◽  
Molecular Mechanisms ◽  
Hydrophobic Interactions ◽  
Substrate Binding ◽  
Interdisciplinary Approach ◽  
Product Formation ◽  
Titration Calorimetry ◽  
Binding Groove ◽  
Dynamics Simulations

Abstract Mannuronan C-5 epimerases catalyse the epimerization of monomer residues in the polysaccharide alginate, changing the physical properties of the biopolymer. The enzymes are utilized to tailor alginate to numerous biological functions by alginate-producing organisms. The underlying molecular mechanisms that control the processive movement of the epimerase along the substrate chain is still elusive. To study this, we have used an interdisciplinary approach combining molecular dynamics simulations with experimental methods from mutant studies of AlgE4, where initial epimerase activity and product formation were addressed with NMR spectroscopy, and characteristics of enzyme-substrate interactions were obtained with isothermal titration calorimetry and optical tweezers. Positive charges lining the substrate-binding groove of AlgE4 appear to control the initial binding of poly-mannuronate, and binding also seems to be mediated by both electrostatic and hydrophobic interactions. After the catalytic reaction, negatively charged enzyme residues might facilitate dissociation of alginate from the positive residues, working like electrostatic switches, allowing the substrate to translocate in the binding groove. Molecular simulations show translocation increments of two monosaccharide units before the next productive binding event resulting in MG-block formation, with the epimerase moving with its N-terminus towards the reducing end of the alginate chain. Our results indicate that the charge pair R343-D345 might be directly involved in conformational changes of a loop that can be important for binding and dissociation. The computational and experimental approaches used in this study complement each other, allowing for a better understanding of individual residues’ roles in binding and movement along the alginate chains.

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