Grana formation: entropy-assisted local order in chloroplasts?

1999 ◽  
Vol 26 (7) ◽  
pp. 641 ◽  
Author(s):  
W. S. Chow
Keyword(s):  
Free Energy ◽  
Short Range ◽  
Protein Complexes ◽  
Minimum Free Energy ◽  
Thylakoid Membranes ◽  
Local Order ◽  
Chlorophyll B ◽  
Van Der Waals Attraction ◽  
Physical Forces ◽  
Fine Tune

Grana formation is a prominent feature of the ultrastructure of chlorophyll b-containing chloroplasts, serving to fine-tune photosynthetic efficiency. This paper examines the physical forces that determine the state of minimum free energy of the chloroplast as manifested by grana formation. In particular, it considers the interplay of van der Waals attraction, electrostatic repulsion and short-range hydration repulsion between thylakoid membranes. In addition to these interactions as determinants of the free energy of the system, it is also proposed that ordering of thylakoid membranes and of intramembrane protein complexes is driven by an increase in the overall entropy of the system. This local order may partly come about by an increase in entropy associated with a greater free volume for diffusion of membrane and stromal components.

scholarly journals How Does the Novel Coronavirus Interact with the Human ACE2 Enzyme? A Thermodynamic Answer

2020 ◽  
Author(s):  
Jones de Andrade ◽  
Paulo Fernando Bruno Gonçalves ◽  
Paulo Augusto Netz
Keyword(s):  
Free Energy ◽  
Protein Complexes ◽  
Minimum Free Energy ◽  
New Drugs ◽  
Host Cells ◽  
Spike Protein ◽  
Health Concern ◽  
Novel Coronavirus ◽  
Dynamics Simulations ◽  
Free Energy Of Binding

<p>The SARS-CoV-2 coronavirus pandemic is certainly the most important public health concern today. Until now there are no vaccines or treatments available, despite intensive international efforts. One of the targets for new drugs is the Coronavirus Spike Protein, responsible for its binding and entry into the host cells. The Receptor Binding Domain (RBD) found at the Spike Protein recognizes the human angiotensin-converting enzyme 2 (hACE2). The present in silico study discuss structural and thermodynamic aspects of the protein complexes involving the RBD’s from the 2002 SARS-CoV and 2019 SARS-CoV-2 with the hACE2. Molecular docking and molecular dynamics simulations of the complexes and isolated proteins were performed, providing insights on their detailed pattern of interactions, and estimating the free energy of binding. The obtained results support previous studies indicating that the chemical affinity of the new SARS-CoV-2 for the hACE2 enzyme virus is much higher than the 2002 SARS-CoV. The herein calculated Gibbs free energy of binding to the hACE2 enzyme is, depending on the technique, from 5.11 kcal/mol to 8.39 kcal/mol more negative in the case of the new coronavirus’ RBD. In addition, within each employed technique, this free energy is consistently 61±2% stronger for SARS-CoV-2 than for SARS-CoV. This work presents a chemical reason for the difficulty in treating the SARS-CoV-2 virus using drugs targeting its Spike Protein, as well as helps to explain its infectivity, while defining a minimum free energy of binding for new drugs to be designed against this disease.<br></p>

scholarly journals How Does the Novel Coronavirus Interact with the Human ACE2 Enzyme? A Thermodynamic Answer

2020 ◽  
Author(s):  
Jones de Andrade ◽  
Paulo Fernando Bruno Gonçalves ◽  
Paulo Augusto Netz
Keyword(s):  
Free Energy ◽  
Protein Complexes ◽  
Minimum Free Energy ◽  
New Drugs ◽  
Host Cells ◽  
Spike Protein ◽  
Health Concern ◽  
Novel Coronavirus ◽  
Dynamics Simulations ◽  
Free Energy Of Binding

<p>The SARS-CoV-2 coronavirus pandemic is certainly the most important public health concern today. Until now there are no vaccines or treatments available, despite intensive international efforts. One of the targets for new drugs is the Coronavirus Spike Protein, responsible for its binding and entry into the host cells. The Receptor Binding Domain (RBD) found at the Spike Protein recognizes the human angiotensin-converting enzyme 2 (hACE2). The present in silico study discuss structural and thermodynamic aspects of the protein complexes involving the RBD’s from the 2002 SARS-CoV and 2019 SARS-CoV-2 with the hACE2. Molecular docking and molecular dynamics simulations of the complexes and isolated proteins were performed, providing insights on their detailed pattern of interactions, and estimating the free energy of binding. The obtained results support previous studies indicating that the chemical affinity of the new SARS-CoV-2 for the hACE2 enzyme virus is much higher than the 2002 SARS-CoV. The herein calculated Gibbs free energy of binding to the hACE2 enzyme is, depending on the technique, from 5.11 kcal/mol to 8.39 kcal/mol more negative in the case of the new coronavirus’ RBD. In addition, within each employed technique, this free energy is consistently 61±2% stronger for SARS-CoV-2 than for SARS-CoV. This work presents a chemical reason for the difficulty in treating the SARS-CoV-2 virus using drugs targeting its Spike Protein, as well as helps to explain its infectivity, while defining a minimum free energy of binding for new drugs to be designed against this disease.<br></p>

scholarly journals How Does the Novel Coronavirus Interact with the Human ACE2 Enzyme? A Thermodynamic Answer

2020 ◽  
Author(s):  
Jones de Andrade ◽  
Paulo Fernando Bruno Gonçalves ◽  
Paulo Augusto Netz
Keyword(s):  
Free Energy ◽  
Protein Complexes ◽  
Minimum Free Energy ◽  
New Drugs ◽  
Host Cells ◽  
Spike Protein ◽  
Health Concern ◽  
Novel Coronavirus ◽  
Dynamics Simulations ◽  
Free Energy Of Binding

<p>The SARS-CoV-2 coronavirus pandemic is certainly the most important public health concern today. Until now there are no vaccines or treatments available, despite intensive international efforts. One of the targets for new drugs is the Coronavirus Spike Protein, responsible for its binding and entry into the host cells. The Receptor Binding Domain (RBD) found at the Spike Protein recognizes the human angiotensin-converting enzyme 2 (hACE2). The present in silico study discuss structural and thermodynamic aspects of the protein complexes involving the RBD’s from the 2002 SARS-CoV and 2019 SARS-CoV-2 with the hACE2. Molecular docking and molecular dynamics simulations of the complexes and isolated proteins were performed, providing insights on their detailed pattern of interactions, and estimating the free energy of binding. The obtained results support previous studies indicating that the chemical affinity of the new SARS-CoV-2 for the hACE2 enzyme virus is much higher than the 2002 SARS-CoV. The herein calculated Gibbs free energy of binding to the hACE2 enzyme is, depending on the technique, from 5.11 kcal/mol to 8.39 kcal/mol more negative in the case of the new coronavirus’ RBD. In addition, within each employed technique, this free energy is consistently 61±2% stronger for SARS-CoV-2 than for SARS-CoV. This work presents a chemical reason for the difficulty in treating the SARS-CoV-2 virus using drugs targeting its Spike Protein, as well as helps to explain its infectivity, while defining a minimum free energy of binding for new drugs to be designed against this disease.<br></p>

Minimum free energy coding for DNA storage

2021 ◽  
pp. 1-1
Author(s):  
Ben Cao ◽  
Xiaokang Zhang ◽  
Jieqiong Wu ◽  
Bin Wang ◽  
Qiang Zhang ◽  
...  
Keyword(s):  
Free Energy ◽  
Minimum Free Energy ◽  
Dna Storage ◽  
Energy Coding

scholarly journals How proteins open fusion pores: insights from molecular simulations

2020 ◽  
Author(s):  
H. Jelger Risselada ◽  
Helmut Grubmüller
Keyword(s):  
Free Energy ◽  
Fusion Proteins ◽  
Graphics Processing Units ◽  
Fusion Reaction ◽  
Molecular Simulations ◽  
Minimum Free Energy ◽  
Free Energy Calculations ◽  
Coarse Grained ◽  
Fusion Pore ◽  
Graphics Processing

AbstractFusion proteins can play a versatile and involved role during all stages of the fusion reaction. Their roles go far beyond forcing the opposing membranes into close proximity to drive stalk formation and fusion. Molecular simulations have played a central role in providing a molecular understanding of how fusion proteins actively overcome the free energy barriers of the fusion reaction up to the expansion of the fusion pore. Unexpectedly, molecular simulations have revealed a preference of the biological fusion reaction to proceed through asymmetric pathways resulting in the formation of, e.g., a stalk-hole complex, rim-pore, or vertex pore. Force-field based molecular simulations are now able to directly resolve the minimum free-energy path in protein-mediated fusion as well as quantifying the free energies of formed reaction intermediates. Ongoing developments in Graphics Processing Units (GPUs), free energy calculations, and coarse-grained force-fields will soon gain additional insights into the diverse roles of fusion proteins.

scholarly journals Probing the biogenesis pathway and dynamics of thylakoid membranes

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Tuomas Huokko ◽  
Tao Ni ◽  
Gregory F. Dykes ◽  
Deborah M. Simpson ◽  
Philip Brownridge ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Photosystem I ◽  
Spatial Organization ◽  
Electron Flux ◽  
Protein Complexes ◽  
Thylakoid Membranes ◽  
Thylakoid Biogenesis ◽  
Photosynthetic Complexes ◽  
Photosynthetic Machinery ◽  
Pcc 7942

AbstractHow thylakoid membranes are generated to form a metabolically active membrane network and how thylakoid membranes orchestrate the insertion and localization of protein complexes for efficient electron flux remain elusive. Here, we develop a method to modulate thylakoid biogenesis in the rod-shaped cyanobacterium Synechococcus elongatus PCC 7942 by modulating light intensity during cell growth, and probe the spatial-temporal stepwise biogenesis process of thylakoid membranes in cells. Our results reveal that the plasma membrane and regularly arranged concentric thylakoid layers have no physical connections. The newly synthesized thylakoid membrane fragments emerge between the plasma membrane and pre-existing thylakoids. Photosystem I monomers appear in the thylakoid membranes earlier than other mature photosystem assemblies, followed by generation of Photosystem I trimers and Photosystem II complexes. Redistribution of photosynthetic complexes during thylakoid biogenesis ensures establishment of the spatial organization of the functional thylakoid network. This study provides insights into the dynamic biogenesis process and maturation of the functional photosynthetic machinery.

scholarly journals Magic number colloidal clusters as minimum free energy structures

2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Junwei Wang ◽  
Chrameh Fru Mbah ◽  
Thomas Przybilla ◽  
Benjamin Apeleo Zubiri ◽  
Erdmann Spiecker ◽  
...  
Keyword(s):  
Free Energy ◽  
Magic Number ◽  
Minimum Free Energy ◽  
Colloidal Clusters

scholarly journals Rock climbing: A local-global algorithm to compute minimum energy and minimum free energy pathways

2017 ◽  
Vol 147 (15) ◽  
pp. 152718 ◽  
Author(s):  
Clark Templeton ◽  
Szu-Hua Chen ◽  
Arman Fathizadeh ◽  
Ron Elber
Keyword(s):  
Free Energy ◽  
Minimum Energy ◽  
Minimum Free Energy ◽  
Rock Climbing ◽  
Global Algorithm ◽  
Energy Pathways
Sign in / Sign up

Export Citation Format

Share Document