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Article ; Online: Sensing membrane voltage by reorientation of dipolar transmembrane peptides.

Bisht, Konark / Lomholt, Michael A / Khandelia, Himanshu

2024 Volume 123, Issue 5, Page(s) 584–597

Abstract: Membrane voltage plays a vital role in the behavior and functions of the lipid bilayer membrane. For instance, it regulates the exchange of molecules across the membrane through transmembrane proteins such as ion channels. In this paper, we study the ... ...

Abstract	Membrane voltage plays a vital role in the behavior and functions of the lipid bilayer membrane. For instance, it regulates the exchange of molecules across the membrane through transmembrane proteins such as ion channels. In this paper, we study the membrane voltage-sensing mechanism, which entails the reorientation of α-helices with a change in the membrane voltage. We consider a helix having a large electrical macrodipole embedded in a lipid bilayer as a model system. We performed extensive molecular dynamics simulations to study the effect of variation of membrane voltage on the tilt angle of peptides and ascertain the optimal parameters for designing such a voltage-sensing peptide. A theoretical model for the system is also developed to investigate the interplay of competing effects of hydrophobic mismatch and dipole-electric field coupling on the tilt of the peptide and further explore the parameter space. This work opens the possibility for the design and fabrication of artificial dipolar membrane voltage-sensing elements for biomedical applications.
MeSH term(s)	Lipid Bilayers/chemistry ; Membrane Proteins/chemistry ; Peptides/chemistry ; Molecular Dynamics Simulation ; Ion Channels/metabolism
Chemical Substances	Lipid Bilayers ; Membrane Proteins ; Peptides ; Ion Channels
Language	English
Publishing date	2024-02-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2024.01.037
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Article ; Online: ATP-Bound State of the Uncoupling Protein 1 (UCP1) from Molecular Simulations.

Jacobsen, Luise / Lydersen, Laura / Khandelia, Himanshu

The journal of physical chemistry. B

2023 Volume 127, Issue 45, Page(s) 9685–9696

Abstract: The uncoupling protein 1 (UCP1) dissipates the transmembrane (TM) proton gradient in the inner mitochondrial membrane (IMM) by leaking protons across the membrane and producing heat in the process. Such a nonshivering production of heat in the brown ... ...

Abstract	The uncoupling protein 1 (UCP1) dissipates the transmembrane (TM) proton gradient in the inner mitochondrial membrane (IMM) by leaking protons across the membrane and producing heat in the process. Such a nonshivering production of heat in the brown adipose tissue can combat obesity-related diseases. UCP1-associated proton leak is activated by free fatty acids and inhibited by purine nucleotides. The mechanism of proton leak and the binding sites of the activators (fatty acids) remain unknown, while the binding site of the inhibitors (nucleotides) was described recently. Using molecular dynamics simulations, we generated a conformational ensemble of UCP1. Using metadynamics-based free energy calculations, we obtained the most likely ATP-bound conformation of UCP1. Our conformational ensemble provides a molecular basis for a breadth of prior biochemical data available for UCP1. Based on the simulations, we make the following testable predictions about the mechanisms of activation of proton leak and proton leak inhibition by ATP: (1) R277 plays the dual role of stabilizing ATP at the binding site for inhibition and acting as a proton surrogate for D28 in the absence of a proton during proton transport, (2) the binding of ATP to UCP1 is mediated by residues R84, R92, R183, and S88, (3) R92 shuttles ATP from the E191-R92 gate in the intermembrane space to the nucleotide binding site and serves to increase ATP affinity, (4) ATP can inhibit proton leak by controlling the ionization states of matrix facing lysine residues such as K269 and K56, and (5) fatty acids can bind to UCP1 from the IMM either via the cavity between TM1 and TM2 or between TM5 and TM6. Our simulations set the platform for future investigations into the proton transport and inhibition mechanisms of UCP1.
MeSH term(s)	Ion Channels/chemistry ; Uncoupling Protein 1/metabolism ; Protons ; Mitochondrial Proteins/chemistry ; Fatty Acids/metabolism ; Nucleotides/metabolism ; Adenosine Triphosphate
Chemical Substances	Ion Channels ; Uncoupling Protein 1 ; Protons ; Mitochondrial Proteins ; Fatty Acids ; Nucleotides ; Adenosine Triphosphate (8L70Q75FXE)
Language	English
Publishing date	2023-11-03
Publishing country	United States
Document type	Journal Article
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.3c03473
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Article ; Online: Interaction of psychedelic tryptamine derivatives with a lipid bilayer.

Zohairi, Fateme / Khandelia, Himanshu / Hakami Zanjani, Ali Asghar

Chemistry and physics of lipids

2023 Volume 251, Page(s) 105279

Abstract: Naturally occurring psychedelics have been used for a long time as remedies or in religious ceremonies and recreational activities. Recent studies have proven the therapeutic potential of some psychedelic compounds to safely treat a wide range of ... ...

Abstract	Naturally occurring psychedelics have been used for a long time as remedies or in religious ceremonies and recreational activities. Recent studies have proven the therapeutic potential of some psychedelic compounds to safely treat a wide range of diseases such as anxiety, depression, migraine, and addiction. It is hypothesized that psychedelic compounds like tryptamines can exert their effects by two possible mechanisms: binding to the transmembrane serotonin receptor and/or modifying the properties of the neuronal membrane that can alter the conformational equilibrium and desensitize receptors. The impact of three different tryptamine class compounds with a tertiary amine (dimethyltryptamine, bufotenine, and 5-MeO-DMT) in both neutral and charged forms on a model bilayer lipid membrane are studied using all-atom MD simulations. All compounds partition into the bilayer, and change membrane properties, but to different extents. We determine the tendency of compounds to partition into the membrane by free energy calculations. Neutral tryptamines partition into the bilayer almost completely. Dimethyltryptamine and 5-MeO-DMT cross the membrane spontaneously during the simulation time, but bufotenine does not, although it has the maximum effect on the structural properties of the membrane. However, protonated compounds partition partially into the bilayer and cannot pass through the middle of the membrane during the simulation time. In this way, subtle alteration of chemical structure can play a significant role in the improvement or deterioration of partitioning of these compounds into the bilayer and their passage across the membrane.
MeSH term(s)	Hallucinogens/pharmacology ; Hallucinogens/therapeutic use ; Bufotenin/metabolism ; Lipid Bilayers ; Tryptamines ; N,N-Dimethyltryptamine ; Methoxydimethyltryptamines/therapeutic use
Chemical Substances	Hallucinogens ; tryptamine (422ZU9N5TV) ; Bufotenin (0A31347TZK) ; Lipid Bilayers ; Tryptamines ; N,N-Dimethyltryptamine (WUB601BHAA) ; Methoxydimethyltryptamines
Language	English
Publishing date	2023-01-07
Publishing country	Ireland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	213869-4
ISSN	1873-2941 ; 0009-3084
ISSN (online)	1873-2941
ISSN	0009-3084
DOI	10.1016/j.chemphyslip.2023.105279
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Article ; Online: EnCurv: Simple Technique of Maintaining Global Membrane Curvature in Molecular Dynamics Simulations.

Yesylevskyy, Semen / Khandelia, Himanshu

Journal of chemical theory and computation

2021 Volume 17, Issue 2, Page(s) 1181–1193

Abstract: The EnCurv method for maintaining membrane curvature in molecular dynamics simulations is introduced. The method allows maintaining any desired curvature in a sector of lipid membrane bent in a single plane without adding any unphysical interactions into ...

Abstract	The EnCurv method for maintaining membrane curvature in molecular dynamics simulations is introduced. The method allows maintaining any desired curvature in a sector of lipid membrane bent in a single plane without adding any unphysical interactions into the system and without restrictions on lateral and transversal lipid diffusion and distribution. The current implementation is limited to the membranes curved in a single plane but generalization to arbitrary curvature and membrane topology is possible. The method is simple, easy to implement, and scales linearly with the system size. EnCurv is agnostic to the force field, simulation parameters, and membrane composition. The proof of principle implementation (https://github.com/yesint/EnCurv) is compatible with the majority of modern simulation packages and shows consistent results on the model systems.
Language	English
Publishing date	2021-01-29
Publishing country	United States
Document type	Journal Article
ISSN	1549-9626
ISSN (online)	1549-9626
DOI	10.1021/acs.jctc.0c00800
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Article ; Online: Bending of a lipid membrane edge by annexin A5 trimers.

Pandey, Mayank Prakash / Telles de Souza, Paulo Cesar / Pezeshkian, Weria / Khandelia, Himanshu

Biophysical journal

2024 Volume 123, Issue 8, Page(s) 1006–1014

Abstract: Plasma membrane damage occurs in healthy cells and more frequently in cancer cells where high growth rates and metastasis result in frequent membrane damage. The annexin family of proteins plays a key role in membrane repair. Annexins are recruited at ... ...

Abstract	Plasma membrane damage occurs in healthy cells and more frequently in cancer cells where high growth rates and metastasis result in frequent membrane damage. The annexin family of proteins plays a key role in membrane repair. Annexins are recruited at the membrane injury site by Ca
MeSH term(s)	Annexin A5/analysis ; Annexin A5/metabolism ; Phosphatidylserines/metabolism ; Cell Membrane/metabolism ; Annexins/analysis ; Annexins/chemistry ; Annexins/metabolism ; Membranes/metabolism
Chemical Substances	Annexin A5 ; Phosphatidylserines ; Annexins
Language	English
Publishing date	2024-03-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2024.03.019
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Zs.A 235: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Specific protonation of acidic residues confers K

Madapally, Hridya Valia / Abe, Kazuhiro / Dubey, Vikas / Khandelia, Himanshu

The Journal of biological chemistry

2023 Volume 300, Issue 1, Page(s) 105542

Abstract: The gastric proton pump ( ... ...

Abstract	The gastric proton pump (H
MeSH term(s)	Potassium/metabolism ; Molecular Dynamics Simulation ; Stomach ; Binding Sites ; Sodium/metabolism ; Adenosine Triphosphatases/metabolism ; Sodium-Potassium-Exchanging ATPase/metabolism ; H(+)-K(+)-Exchanging ATPase/genetics ; H(+)-K(+)-Exchanging ATPase/metabolism
Chemical Substances	Potassium (RWP5GA015D) ; Sodium (9NEZ333N27) ; Adenosine Triphosphatases (EC 3.6.1.-) ; Sodium-Potassium-Exchanging ATPase (EC 7.2.2.13) ; H(+)-K(+)-Exchanging ATPase (EC 3.6.3.10)
Language	English
Publishing date	2023-12-10
Publishing country	United States
Document type	Journal Article
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2023.105542
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Article ; Online: Molecular Mechanism of Hydrotropic Properties of GTP and ATP.

Pandey, Mayank Prakash / Sasidharan, Sreeja / Raghunathan, Velayudhan A / Khandelia, Himanshu

The journal of physical chemistry. B

2022 Volume 126, Issue 42, Page(s) 8486–8494

Abstract: Hydrotropes are small amphiphilic compounds that increase the aqueous solubility of hydrophobic molecules. Recent evidence suggests that adenosine triphosphate (ATP), which is the primary energy carrier in cells, also assumes hydrotropic properties to ... ...

Abstract	Hydrotropes are small amphiphilic compounds that increase the aqueous solubility of hydrophobic molecules. Recent evidence suggests that adenosine triphosphate (ATP), which is the primary energy carrier in cells, also assumes hydrotropic properties to prevent the aggregation of hydrophobic proteins, but the mechanism of hydrotropy is unknown. Here, we compare the hydrotropic behavior of all four biological nucleoside triphosphates (NTPs) using molecular dynamics (MD) simulations. We launch all atom MD simulations of aqueous solutions of NTPs [ATP, guanosine triphosphate (GTP), cytidine triphosphate (CTP), and uridine triphosphate (UTP)] with pyrene, which acts both as a model hydrophobic compound and as a spectroscopic reporter for aggregation. GTP prevents pyrene aggregation effectively. Dissolution is not achieved in the presence of CTP and UTP. The higher stability of the base stacking in guanine is responsible for the higher hydrotropic efficiency of GTP. Consistent with the simulations, spectroscopic measurements also suggest that the hydrotropic activity of GTP is higher than ATP. Stacking of aromatic pyrene with the aromatic base of NTPs is a characteristic feature of this hydrotropic property. Both ATP and GTP also dissolve clusters of di- and tripeptides containing tryptophan but with equal potency. Importantly, the presence of aromatic amino acids is a necessary condition for the hydrotropic potency of ATP and GTP. Our results can have broad implications for hydrotrope design in the pharmaceutical industry, as well as the possibility of cells employing GTP as a hydrotrope to regulate the hydrophobic protein aggregation in membrane-less biological condensates.
MeSH term(s)	Guanosine Triphosphate/metabolism ; Uridine Triphosphate ; Adenosine Triphosphate/metabolism ; Cytidine Triphosphate ; Protein Aggregates ; Tryptophan ; Nucleosides ; Pyrenes ; Guanine
Chemical Substances	Guanosine Triphosphate (86-01-1) ; Uridine Triphosphate (UT0S826Z60) ; Adenosine Triphosphate (8L70Q75FXE) ; Cytidine Triphosphate (65-47-4) ; Protein Aggregates ; Tryptophan (8DUH1N11BX) ; Nucleosides ; Pyrenes ; Guanine (5Z93L87A1R)
Language	English
Publishing date	2022-10-17
Publishing country	United States
Document type	Journal Article
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.2c06077
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Article ; Online: The molecular basis of the antidepressant action of the magic mushroom extract, psilocin.

Hakami Zanjani, Ali Asghar / Nguyen, Teresa Quynh Tram / Jacobsen, Luise / Khandelia, Himanshu

Biochimica et biophysica acta. Proteins and proteomics

2023 Volume 1871, Issue 4, Page(s) 140914

Abstract: Magic mushrooms, and their extract psilocybin, are well-known for their psychedelic properties and recreational use. Psilocin, the bio-active form of psilocybin, can potentially treat various psychiatric diseases. Psilocin putatively exerts its ... ...

Abstract	Magic mushrooms, and their extract psilocybin, are well-known for their psychedelic properties and recreational use. Psilocin, the bio-active form of psilocybin, can potentially treat various psychiatric diseases. Psilocin putatively exerts its psychedelic effect as an agonist to the serotonin 2A receptor (5-HT
MeSH term(s)	Psilocybin ; Hallucinogens/pharmacology ; Hallucinogens/chemistry ; Serotonin ; Amines
Chemical Substances	psilocin (CMS88KUW0G) ; Psilocybin (2RV7212BP0) ; Hallucinogens ; Serotonin (333DO1RDJY) ; Amines
Language	English
Publishing date	2023-04-03
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2918798-9
ISSN	1878-1454 ; 1570-9639
ISSN (online)	1878-1454
ISSN	1570-9639
DOI	10.1016/j.bbapap.2023.140914
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Article ; Online: Phospholamban inhibits the cardiac calcium pump by interrupting an allosteric activation pathway.

Cleary, Sean R / Seflova, Jaroslava / Cho, Ellen E / Bisht, Konark / Khandelia, Himanshu / Espinoza-Fonseca, L Michel / Robia, Seth L

The Journal of biological chemistry

2024 , Page(s) 107267

Abstract: Phospholamban (PLB) is a transmembrane micropeptide that regulates the ... ...

Abstract	Phospholamban (PLB) is a transmembrane micropeptide that regulates the Ca
Language	English
Publishing date	2024-04-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2024.107267
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Uc I Zs.108: Show issues

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Article ; Online: Drastic differences between the release kinetics of two highly related porphyrins in liposomal membranes: mTHPP and pTHPP

Kuntsche, Judith / Rajakulendran, Kirishana / Sabriye, Hibo Mohamed Takane / Tawakal, Navidullah / Khandelia, Himanshu / Hakami Zanjani, Ali Asghar

Journal of Colloid And Interface Science. 2023 Dec., v. 651 p.750-759

2023

Abstract: The release of hydrophobic compounds from liposomal membranes occurs by partitioning and is thus determined by the physicochemical properties (e.g. logP and water solubility) of the drug. We postulate that even minor structural differences, e.g. the ... ...

Abstract	The release of hydrophobic compounds from liposomal membranes occurs by partitioning and is thus determined by the physicochemical properties (e.g. logP and water solubility) of the drug. We postulate that even minor structural differences, e.g. the position of the phenolic OH-group of the hydrophobic porphyrins mTHPP and pTHPP (meta vs. para substitution), distinctly affect their partitioning and release behavior from liposomes. The release and redistribution of mTHPP and pTHPP from lecithin or POPC/POPG liposomes to different acceptor particles (DSPE-mPEG micelles and liposomes) was studied by asymmetrical flow field-flow fractionation to separate donor and acceptor particles. Reversed phase HPLC was applied to detect differences in partitioning. Molecular dynamics (MD) simulations were carried out to obtain molecular insight in the different behavior of the two compounds inside a lipid bilayer. Despite the minor differences in chemical structure, mTHPP is more hydrophobic and redistributes much slower to both acceptor phases than pTHPP. MD simulations indicate that compared to pTHPP, mTHPP makes stronger hydrogen bonds with the lipid head groups, is oriented more parallel to the lipid tails and is embedded slightly deeper in the membrane.
Keywords	chemical structure ; drugs ; fractionation ; hydrogen ; hydrophobicity ; lecithins ; lipid bilayers ; micelles ; molecular dynamics ; reversed-phase high performance liquid chromatography ; water solubility ; Liposomes ; Porphyrin ; Drug release ; Partitioning ; Molecular dynamics simulation ; AF4 ; DLPC ; DLS ; DPPC ; DPPG ; DSPE-mPEG ; HPLC ; LS ; MALS ; MD ; mTHPC ; mTHPP ; MWCO ; PdI ; POPC ; POPG ; pTHPP ; RDF ; VMD ; VWD
Language	English
Dates of publication	2023-12
Size	p. 750-759.
Publishing place	Elsevier Inc.
Document type	Article ; Online
ZDB-ID	241597-5
ISSN	1095-7103 ; 0021-9797
ISSN (online)	1095-7103
ISSN	0021-9797
DOI	10.1016/j.jcis.2023.07.152
Database	NAL-Catalogue (AGRICOLA)

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