scholarly journals Re-charging your fats: Charmm36 parameters for neutral lipids triacylglycerol and diacylglycerol

2021 ◽  
Author(s):  
Pablo Campomanes ◽  
Janak Prabhu ◽  
Valeria Zoni ◽  
Stefano Vanni
Keyword(s):  
Neutral Lipids ◽  
Md Simulations ◽  
Interfacial Properties ◽  
Lipid Storage ◽  
Intracellular Lipid ◽  
Structural Investigations ◽  
Glycerol Ester ◽  
Cellular Lipids ◽  
Lipid Assemblies ◽  
Chemical Groups

Neutral lipids (NLs) are an abundant class of cellular lipids. They are characterized by the total lack of charged chemical groups in their structure, and, as a consequence, they play a major role in intracellular lipid storage. NLs that carry a glycerol backbone, such as triacylglycerols (TGs) and diacylglycerols (DGs), are also involved in the biosynthetic pathway of cellular phospholipids, and they have recently been the subject of numerous structural investigations by means of atomistic molecular dynamics (MD) simulations. However, conflicting results on the physicochemical behavior of NLs were observed depending on the nature of the atomistic force field used. Here, we show that current phospholipid-derived CHARMM36 parameters for DGs and TGs cannot reproduce adequately interfacial properties of these NLs, due to excessive hydrophilicity at the glycerol-ester region. By following a CHARMM36-consistent parameterization strategy, we develop new parameters for both TGs and DGs that are compatible with both cutoff- based and Particle Mesh Ewald (PME) schemes for the treatment of Lennard Jones interactions. We show that our new parameters can reproduce interfacial properties of NLs and their behavior in more complex lipid assemblies. We discuss the implications of our findings in the context of intracellular lipid storage and NLs cellular activity.

Structural insights into the repair mechanism of AGT for methyl-induced DNA damage

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Rajendra P. Koirala ◽  
Rudramani Pokhrel ◽  
Prabin Baral ◽  
Purushottam B. Tiwari ◽  
Prem P. Chapagain ◽  
...  
Keyword(s):  
Covalent Bond ◽  
Cancer Therapeutics ◽  
Md Simulations ◽  
Structural Features ◽  
Umbrella Sampling ◽  
Repair Mechanism ◽  
Structural Investigations ◽  
Methylated Dna ◽  
Dna Base ◽  
Dna Alkyltransferase

Abstract Methylation induced DNA base-pairing damage is one of the major causes of cancer. O6-alkylguanine-DNA alkyltransferase (AGT) is considered a demethylation agent of the methylated DNA. Structural investigations with thermodynamic properties of the AGT-DNA complex are still lacking. In this report, we modeled two catalytic states of AGT-DNA interactions and an AGT-DNA covalent complex and explored structural features using molecular dynamics (MD) simulations. We utilized the umbrella sampling method to investigate the changes in the free energy of the interactions in two different AGT-DNA catalytic states, one with methylated GUA in DNA and the other with methylated CYS145 in AGT. These non-covalent complexes represent the pre- and post-repair complexes. Therefore, our study encompasses the process of recognition, complex formation, and separation of the AGT and the damaged (methylated) DNA base. We believe that the use of parameters for the amino acid and nucleotide modifications and for the protein-DNA covalent bond will allow investigations of the DNA repair mechanism as well as the exploration of cancer therapeutics targeting the AGT-DNA complexes at various functional states as well as explorations via stabilization of the complex.

scholarly journals Ferroptotic cell death triggered by conjugated linolenic acids is mediated by ACSL1

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Alexander Beatty ◽  
Tanu Singh ◽  
Yulia Y. Tyurina ◽  
Vladimir A. Tyurin ◽  
Svetlana Samovich ◽  
...  
Keyword(s):  
Cell Death ◽  
Therapeutic Potential ◽  
Neutral Lipids ◽  
Cell Types ◽  
Lipid Hydroperoxides ◽  
Conjugated Linolenic Acids ◽  
Cellular Lipids ◽  
Transcriptional Changes ◽  
Acyl Chains ◽  
Tumor Growth And Metastasis

AbstractFerroptosis is associated with lipid hydroperoxides generated by the oxidation of polyunsaturated acyl chains. Lipid hydroperoxides are reduced by glutathione peroxidase 4 (GPX4) and GPX4 inhibitors induce ferroptosis. However, the therapeutic potential of triggering ferroptosis in cancer cells with polyunsaturated fatty acids is unknown. Here, we identify conjugated linoleates including α-eleostearic acid (αESA) as ferroptosis inducers. αESA does not alter GPX4 activity but is incorporated into cellular lipids and promotes lipid peroxidation and cell death in diverse cancer cell types. αESA-triggered death is mediated by acyl-CoA synthetase long-chain isoform 1, which promotes αESA incorporation into neutral lipids including triacylglycerols. Interfering with triacylglycerol biosynthesis suppresses ferroptosis triggered by αESA but not by GPX4 inhibition. Oral administration of tung oil, naturally rich in αESA, to mice limits tumor growth and metastasis with transcriptional changes consistent with ferroptosis. Overall, these findings illuminate a potential approach to ferroptosis, complementary to GPX4 inhibition.

scholarly journals Structural flexibility at a major conserved antibody target on hepatitis C virus E2 antigen

2016 ◽  
Vol 113 (45) ◽  
pp. 12768-12773 ◽  
Author(s):  
Leopold Kong ◽  
David E. Lee ◽  
Rameshwar U. Kadam ◽  
Tong Liu ◽  
Erick Giang ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Viral Entry ◽  
Neutralizing Antibodies ◽  
Vaccine Design ◽  
Neutralizing Antibody ◽  
Md Simulations ◽  
Receptor Binding Site ◽  
Structural Investigations ◽  
Thermophilic Organisms

Hepatitis C virus (HCV) is a major cause of liver disease, affecting over 2% of the world’s population. The HCV envelope glycoproteins E1 and E2 mediate viral entry, with E2 being the main target of neutralizing antibody responses. Structural investigations of E2 have produced templates for vaccine design, including the conserved CD81 receptor-binding site (CD81bs) that is a key target of broadly neutralizing antibodies (bNAbs). Unfortunately, immunization with recombinant E2 and E1E2 rarely elicits sufficient levels of bNAbs for protection. To understand the challenges for eliciting bNAb responses against the CD81bs, we investigated the E2 CD81bs by electron microscopy (EM), hydrogen–deuterium exchange (HDX), molecular dynamics (MD), and calorimetry. By EM, we observed that HCV1, a bNAb recognizing the N-terminal region of the CD81bs, bound a soluble E2 core construct from multiple angles of approach, suggesting components of the CD81bs are flexible. HDX of multiple E2 constructs consistently indicated the entire CD81bs was flexible relative to the rest of the E2 protein, which was further confirmed by MD simulations. However, E2 has a high melting temperature of 84.8 °C, which is more akin to proteins from thermophilic organisms. Thus, recombinant E2 is a highly stable protein overall, but with an exceptionally flexible CD81bs. Such flexibility may promote induction of nonneutralizing antibodies over bNAbs to E2 CD81bs, underscoring the necessity of rigidifying this antigenic region as a target for rational vaccine design.

scholarly journals A Unique Junctional Interface at Contact Sites Between the Endoplasmic Reticulum and Lipid Droplets

2021 ◽  
Vol 9 ◽  
Author(s):  
Vineet Choudhary ◽  
Roger Schneiter
Keyword(s):  
Endoplasmic Reticulum ◽  
Lipid Droplets ◽  
Neutral Lipids ◽  
Close Contact ◽  
Lipid Storage ◽  
Metabolic Energy ◽  
Lipid Monolayer ◽  
Storage Diseases ◽  
Contact Sites ◽  
Ordered Assembly

Lipid droplets (LDs) constitute compartments dedicated to the storage of metabolic energy in the form of neutral lipids. LDs originate from the endoplasmic reticulum (ER) with which they maintain close contact throughout their life cycle. These ER–LD junctions facilitate the exchange of both proteins and lipids between these two compartments. In recent years, proteins that are important for the proper formation of LDs and localize to ER–LD junctions have been identified. This junction is unique as it is generally believed to invoke a transition from the ER bilayer membrane to a lipid monolayer that delineates LDs. Proper formation of this junction requires the ordered assembly of proteins and lipids at specialized ER subdomains. Without such a well-ordered assembly of LD biogenesis factors, neutral lipids are synthesized throughout the ER membrane, resulting in the formation of aberrant LDs. Such ectopically formed LDs impact ER and lipid homeostasis, resulting in different types of lipid storage diseases. In response to starvation, the ER–LD junction recruits factors that tether the vacuole to these junctions to facilitate LD degradation. In addition, LDs maintain close contacts with peroxisomes and mitochondria for metabolic channeling of the released fatty acids toward beta-oxidation. In this review, we discuss the function of different components that ensure proper functioning of LD contact sites, their role in lipogenesis and lipolysis, and their relation to lipid storage diseases.

Interfacial anomaly in low global warming potential refrigerant blends as predicted by molecular dynamics simulations

2019 ◽  
Vol 21 (39) ◽  
pp. 22092-22102 ◽  
Author(s):  
Yuting Li ◽  
Wael A. Fouad ◽  
Lourdes F. Vega
Keyword(s):  
Molecular Dynamics ◽  
Global Warming ◽  
Molecular Dynamics Simulations ◽  
Global Warming Potential ◽  
Md Simulations ◽  
Interfacial Properties ◽  
Anomalous Behavior ◽  
Dynamics Simulations ◽  
Low Global Warming Potential

Anomalous behavior of the interfacial properties of low GWP refrigerants predicted by MD simulations.

scholarly journals Metabolism of neutral lipids in cultured fibroblasts from multisystemic (or type 3) lipid storage myopathy

1987 ◽  
Vol 164 (3) ◽  
pp. 703-708 ◽  
Author(s):  
Jean RADOM ◽  
Robert SALVAYRE ◽  
Anne NEGRE ◽  
Arlette MARET ◽  
Louis DOUSTE-BLAZY
Keyword(s):  
Neutral Lipids ◽  
Lipid Storage ◽  
Lipid Storage Myopathy ◽  
Cultured Fibroblasts ◽  
Type 3

scholarly journals Bovine Cumulus Cells Protect Maturing Oocytes from Increased Fatty Acid Levels by Massive Intracellular Lipid Storage

2013 ◽  
Vol 88 (6) ◽  
pp. 164-164 ◽  
Author(s):  
H. Aardema ◽  
F. Lolicato ◽  
C. H. A. van de Lest ◽  
J. F. Brouwers ◽  
A. B. Vaandrager ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Cumulus Cells ◽  
Lipid Storage ◽  
Intracellular Lipid

Glycerol-Ester Hydrolase from Human Small Intestine and Its Possible Role in the Degradation of Neutral Lipids

Digestion ◽  
1977 ◽  
Vol 16 (1-2) ◽  
pp. 146-159 ◽  
Author(s):  
R. Négrel ◽  
G. Serrero ◽  
G. Ailhaud ◽  
J.-F. Rey ◽  
J. Delmont
Keyword(s):  
Small Intestine ◽  
Neutral Lipids ◽  
Human Small Intestine ◽  
Ester Hydrolase ◽  
Glycerol Ester

scholarly journals Regulation of fibroblast lipid storage and myofibroblast phenotypes during alveolar septation in mice

2014 ◽  
Vol 307 (8) ◽  
pp. L618-L631 ◽  
Author(s):  
Stephen E. McGowan ◽  
Diann M. McCoy
Keyword(s):  
Gene Expression ◽  
Neutral Lipids ◽  
Growth Factor Receptor ◽  
Lipid Storage ◽  
Lung Fibroblasts ◽  
Peroxisome Proliferator ◽  
Peroxisome Proliferator Activated Receptor ◽  
Mesenchymal Progenitors ◽  
Storage Cells ◽  
Lung Regeneration

Signaling through platelet-derived growth factor receptor-α (PDGFRα) is required for alveolar septation and participates in alveolar regeneration after pneumonectomy. In both adipose tissue and skeletal muscle, bipotent pdgfrα-expressing progenitors expressing delta-like ligand-1 or sex-determining region Y box 9 (Sox9) may differentiate into either lipid storage cells or myofibroblasts. We analyzed markers of mesenchymal progenitors and differentiation in lung fibroblasts (LF) with different levels (absent, low, or high) of pdgfrα gene expression. A larger proportion of pdgfrα-expressing than nonexpressing LF contained Sox9. Neutral lipids, CD166, and Tcf21 were more abundant in LF with a lower compared with a higher level of pdgfrα gene expression. PDGF-A increased Sox9 in primary LF cultures, suggesting that active signaling through PDGFRα is required to maintain Sox9. As alveolar septation progresses from postnatal day (P) 8 to P12, fewer pdgfrα-expressing LF contain Sox9, whereas more of these LF contain myocardin-like transcription factor-A, showing that Sox9 diminishes as LF become myofibroblasts. At P8, neutral lipid droplets predominate in LF with the lower level of pdgfrα gene expression, whereas transgelin ( tagln) was predominantly expressed in LF with higher pdgfrα gene expression. Targeted deletion of pdgfrα in LF, which expressed tagln, reduced Sox9 in α-actin (α-SMA, ACTA2)-containing LF, whereas it increased the abundance of cell surface delta-like protein-1 (as well as peroxisome proliferator-activated receptor-γ and tcf21 mRNA in LF, which also expressed stem cell antigen-1). Thus pdgfrα deletion differentially alters delta-like protein-1 and Sox9, suggesting that targeting different downstream pathways in PDGF-A-responsive LF could identify strategies that promote lung regeneration without initiating fibrosis.

Sign in / Sign up

Export Citation Format

Share Document