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Article ; Online: Structural basis for defective membrane targeting of mutant enzyme in human VLCAD deficiency.

Prew, Michelle S / Camara, Christina M / Botzanowski, Thomas / Moroco, Jamie A / Bloch, Noah B / Levy, Hannah R / Seo, Hyuk-Soo / Dhe-Paganon, Sirano / Bird, Gregory H / Herce, Henry D / Gygi, Micah A / Escudero, Silvia / Wales, Thomas E / Engen, John R / Walensky, Loren D

Nature communications

2022 Volume 13, Issue 1, Page(s) 3669

Abstract: Very long-chain acyl-CoA dehydrogenase (VLCAD) is an inner mitochondrial membrane enzyme that catalyzes the first and rate-limiting step of long-chain fatty acid oxidation. Point mutations in human VLCAD can produce an inborn error of metabolism called ... ...

Abstract	Very long-chain acyl-CoA dehydrogenase (VLCAD) is an inner mitochondrial membrane enzyme that catalyzes the first and rate-limiting step of long-chain fatty acid oxidation. Point mutations in human VLCAD can produce an inborn error of metabolism called VLCAD deficiency that can lead to severe pathophysiologic consequences, including cardiomyopathy, hypoglycemia, and rhabdomyolysis. Discrete mutations in a structurally-uncharacterized C-terminal domain region of VLCAD cause enzymatic deficiency by an incompletely defined mechanism. Here, we conducted a structure-function study, incorporating X-ray crystallography, hydrogen-deuterium exchange mass spectrometry, computational modeling, and biochemical analyses, to characterize a specific membrane interaction defect of full-length, human VLCAD bearing the clinically-observed mutations, A450P or L462P. By disrupting a predicted α-helical hairpin, these mutations either partially or completely impair direct interaction with the membrane itself. Thus, our data support a structural basis for VLCAD deficiency in patients with discrete mutations in an α-helical membrane-binding motif, resulting in pathologic enzyme mislocalization.
MeSH term(s)	Acyl-CoA Dehydrogenase, Long-Chain/genetics ; Acyl-CoA Dehydrogenase, Long-Chain/metabolism ; Congenital Bone Marrow Failure Syndromes/genetics ; Humans ; Lipid Metabolism, Inborn Errors/genetics ; Lipid Metabolism, Inborn Errors/metabolism ; Mitochondrial Diseases/genetics ; Muscular Diseases
Chemical Substances	Acyl-CoA Dehydrogenase, Long-Chain (EC 1.3.8.8)
Language	English
Publishing date	2022-06-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-31466-2
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Visualization of the Nucleolus in Living Cells with Cell-Penetrating Fluorescent Peptides.

Martin, Robert M / Herce, Henry D / Ludwig, Anne K / Cardoso, M Cristina

Methods in molecular biology (Clifton, N.J.)

2016 Volume 1455, Page(s) 71–82

Abstract: The nucleolus is the hallmark of nuclear compartmentalization and has been shown to exert multiple roles in cellular metabolism besides its main function as the place of ribosomal RNA synthesis and assembly of ribosomes. The nucleolus plays also a major ... ...

Abstract	The nucleolus is the hallmark of nuclear compartmentalization and has been shown to exert multiple roles in cellular metabolism besides its main function as the place of ribosomal RNA synthesis and assembly of ribosomes. The nucleolus plays also a major role in nuclear organization as the largest compartment within the nucleus. The prominent structure of the nucleolus can be detected using contrast light microscopy providing an approximate localization of the nucleolus, but this approach does not allow to determine accurately the three-dimensional structure of the nucleolus in cells and tissues. Immunofluorescence staining with antibodies specific to nucleolar proteins albeit very useful is time consuming, normally antibodies recognize their epitopes only within a small range of species and is applicable only in fixed cells. Here, we present a simple method to selectively and accurately label this ubiquitous subnuclear compartment in living cells of a large range of species using a fluorescently labeled cell-penetrating peptide.
Language	English
Publishing date	2016
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-3792-9_6
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Article ; Online: Design of stapled antimicrobial peptides that are stable, nontoxic and kill antibiotic-resistant bacteria in mice.

Mourtada, Rida / Herce, Henry D / Yin, Daniel J / Moroco, Jamie A / Wales, Thomas E / Engen, John R / Walensky, Loren D

Nature biotechnology

2019 Volume 37, Issue 10, Page(s) 1186–1197

Abstract: The clinical translation of cationic α-helical antimicrobial peptides (AMPs) has been hindered by structural instability, proteolytic degradation and in vivo toxicity from nonspecific membrane lysis. Although analyses of hydrophobic content and charge ... ...

Abstract	The clinical translation of cationic α-helical antimicrobial peptides (AMPs) has been hindered by structural instability, proteolytic degradation and in vivo toxicity from nonspecific membrane lysis. Although analyses of hydrophobic content and charge distribution have informed the design of synthetic AMPs with increased potency and reduced in vitro hemolysis, nonspecific membrane toxicity in vivo continues to impede AMP drug development. Here, we analyzed a 58-member library of stapled AMPs (StAMPs) based on magainin II and applied the insights from structure-function-toxicity measurements to devise an algorithm for the design of stable, protease-resistant, potent and nontoxic StAMP prototypes. We show that a lead double-stapled StAMP named Mag(i+4)1,15(A9K,B21A,N22K,S23K) can kill multidrug-resistant Gram-negative pathogens, such as colistin-resistant Acinetobacter baumannii in a mouse peritonitis-sepsis model, without observed hemolysis or renal injury in murine toxicity studies. Inputting the amino acid sequences alone, we further generated membrane-selective StAMPs of pleurocidin, CAP18 and esculentin, highlighting the generalizability of our design platform.
MeSH term(s)	Animals ; Anti-Bacterial Agents ; Antimicrobial Cationic Peptides/chemical synthesis ; Bacteria/drug effects ; Cell Line ; Drug Design ; Drug Resistance, Bacterial ; Erythrocytes/drug effects ; Female ; Humans ; Male ; Mice ; Mice, Inbred C57BL ; Peritonitis/drug therapy ; Peritonitis/microbiology ; Sepsis/drug therapy ; Sepsis/microbiology
Chemical Substances	Anti-Bacterial Agents ; Antimicrobial Cationic Peptides
Language	English
Publishing date	2019-08-19
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1311932-1
ISSN	1546-1696 ; 1087-0156
ISSN (online)	1546-1696
ISSN	1087-0156
DOI	10.1038/s41587-019-0222-z
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Zs.A 2167: 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: Fundamental molecular mechanism for the cellular uptake of guanidinium-rich molecules.

Herce, Henry D / Garcia, Angel E / Cardoso, M Cristina

Journal of the American Chemical Society

2014 Volume 136, Issue 50, Page(s) 17459–17467

Abstract: Guanidinium-rich molecules, such as cell-penetrating peptides, efficiently enter living cells in a non-endocytic energy-independent manner and transport a wide range of cargos, including drugs and biomarkers. The mechanism by which these highly cationic ... ...

Abstract	Guanidinium-rich molecules, such as cell-penetrating peptides, efficiently enter living cells in a non-endocytic energy-independent manner and transport a wide range of cargos, including drugs and biomarkers. The mechanism by which these highly cationic molecules efficiently cross the hydrophobic barrier imposed by the plasma membrane remains a fundamental open question. Here, a combination of computational results and in vitro and live-cell experimental evidence reveals an efficient energy-independent translocation mechanism for arginine-rich molecules. This mechanism unveils the essential role of guanidinium groups and two universal cell components: fatty acids and the cell membrane pH gradient. Deprotonated fatty acids in contact with the cell exterior interact with guanidinium groups, leading to a transient membrane channel that facilitates the transport of arginine-rich peptides toward the cell interior. On the cytosolic side, the fatty acids become protonated, releasing the peptides and resealing the channel. This fundamental mechanism appears to be universal across cells from different species and kingdoms.
MeSH term(s)	Cell-Penetrating Peptides/chemistry ; Cell-Penetrating Peptides/metabolism ; Cells, Cultured ; Computer Simulation ; Fatty Acids/chemistry ; Guanidine/chemistry ; Guanidine/metabolism ; Humans ; Hydrogen-Ion Concentration ; Hydrophobic and Hydrophilic Interactions
Chemical Substances	Cell-Penetrating Peptides ; Fatty Acids ; Guanidine (JU58VJ6Y3B)
Language	English
Publishing date	2014-12-17
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/ja507790z
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Article ; Online: Can Specific Protein-Lipid Interactions Stabilize an Active State of the Beta 2 Adrenergic Receptor?

Neale, Chris / Herce, Henry D / Pomès, Régis / García, Angel E

Biophysical journal

2015 Volume 109, Issue 8, Page(s) 1652–1662

Abstract: G-protein-coupled receptors are eukaryotic membrane proteins with broad biological and pharmacological relevance. Like all membrane-embedded proteins, their location and orientation are influenced by lipids, which can also impact protein function via ... ...

Abstract	G-protein-coupled receptors are eukaryotic membrane proteins with broad biological and pharmacological relevance. Like all membrane-embedded proteins, their location and orientation are influenced by lipids, which can also impact protein function via specific interactions. Extensive simulations totaling 0.25 ms reveal a process in which phospholipids from the membrane's cytosolic leaflet enter the empty G-protein binding site of an activated β2 adrenergic receptor and form salt-bridge interactions that inhibit ionic lock formation and prolong active-state residency. Simulations of the receptor embedded in an anionic membrane show increased lipid binding, providing a molecular mechanism for the experimental observation that anionic lipids can enhance receptor activity. Conservation of the arginine component of the ionic lock among Rhodopsin-like G-protein-coupled receptors suggests that intracellular lipid ingression between receptor helices H6 and H7 may be a general mechanism for active-state stabilization.
MeSH term(s)	Binding Sites ; Carbon/chemistry ; Humans ; Lipid Bilayers/chemistry ; Molecular Dynamics Simulation ; Mutation ; Oxygen/chemistry ; Phosphatidylcholines/chemistry ; Phosphatidylglycerols/chemistry ; Protein Conformation ; Protein Stability ; Receptors, Adrenergic, beta-2/genetics ; Receptors, Adrenergic, beta-2/metabolism
Chemical Substances	Lipid Bilayers ; Phosphatidylcholines ; Phosphatidylglycerols ; Receptors, Adrenergic, beta-2 ; Carbon (7440-44-0) ; 1-palmitoyl-2-oleoylglycero-3-phosphoglycerol (81490-05-3) ; Oxygen (S88TT14065) ; 1-palmitoyl-2-oleoylphosphatidylcholine (TE895536Y5)
Language	English
Publishing date	2015-10-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2015.08.028
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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)
Zs.MO 2: Show issues

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Article ; Online: Targeting a helix-in-groove interaction between E1 and E2 blocks ubiquitin transfer.

Cathcart, Ann M / Bird, Gregory H / Wales, Thomas E / Herce, Henry D / Harvey, Edward P / Hauseman, Zachary J / Newman, Catherine E / Adhikary, Utsarga / Prew, Michelle S / Oo, Tun / Lee, Susan / Engen, John R / Walensky, Loren D

Nature chemical biology

2020 Volume 16, Issue 11, Page(s) 1218–1226

Abstract: The ubiquitin-proteasome system (UPS) is a highly regulated protein disposal process critical to cell survival. Inhibiting the pathway induces proteotoxic stress and can be an effective cancer treatment. The therapeutic window observed upon proteasomal ... ...

Abstract	The ubiquitin-proteasome system (UPS) is a highly regulated protein disposal process critical to cell survival. Inhibiting the pathway induces proteotoxic stress and can be an effective cancer treatment. The therapeutic window observed upon proteasomal blockade has motivated multiple UPS-targeting strategies, including preventing ubiquitination altogether. E1 initiates the cascade by transferring ubiquitin to E2 enzymes. A small molecule that engages the E1 ATP-binding site and derivatizes ubiquitin disrupts enzymatic activity and kills cancer cells. However, binding-site mutations cause resistance, motivating alternative approaches to block this promising target. We identified an interaction between the E2 N-terminal alpha-1 helix and a pocket within the E1 ubiquitin-fold domain as a potentially druggable site. Stapled peptides modeled after the E2 alpha-1 helix bound to the E1 groove, induced a consequential conformational change and inhibited E1 ubiquitin thiotransfer, disrupting E2 ubiquitin charging and ubiquitination of cellular proteins. Thus, we provide a blueprint for a distinct E1-targeting strategy to treat cancer.
MeSH term(s)	Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Binding Sites ; Cell Line, Tumor ; Drug Design ; Drug Resistance, Neoplasm ; Humans ; Molecular Conformation ; Molecular Docking Simulation ; Peptides/chemistry ; Proteasome Endopeptidase Complex/metabolism ; Protein Binding ; Structure-Activity Relationship ; Ubiquitin/chemistry ; Ubiquitin/genetics ; Ubiquitin/metabolism ; Ubiquitin-Activating Enzymes/metabolism ; Ubiquitination
Chemical Substances	Peptides ; UBA1 protein, human ; Ubiquitin ; Adenosine Triphosphate (8L70Q75FXE) ; Proteasome Endopeptidase Complex (EC 3.4.25.1) ; UBA7 protein, human (EC 6.2.1.45) ; Ubiquitin-Activating Enzymes (EC 6.2.1.45)
Language	English
Publishing date	2020-08-17
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2202962-X
ISSN	1552-4469 ; 1552-4450
ISSN (online)	1552-4469
ISSN	1552-4450
DOI	10.1038/s41589-020-0625-7
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Zs.A 6251: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular ab Jg. 2022: Lesesaal (EG)
Zs.MG 90: Show issues

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Article: Cell penetrating peptides: how do they do it?

Herce, Henry D / Garcia, Angel E

Journal of biological physics

2008 Volume 33, Issue 5-6, Page(s) 345–356

Abstract: ... interactions (Herce and Garcia, PNAS, 104: 20805 (2007) [1]). It involves the translocation of charged residues ...

Abstract	Cell penetrating peptides consist of short sequences of amino acids containing a large net positive charge that are able to penetrate almost any cell, carrying with them relatively large cargoes such as proteins, oligonucleotides, and drugs. During the 10 years since their discovery, the question of how they manage to translocate across the membrane has remained unanswered. The main discussion has been centered on whether they follow an energy-independent or an energy-dependent pathway. Recently, we have discovered the possibility of an energy-independent pathway that challenges fundamental concepts associated with protein-membrane interactions (Herce and Garcia, PNAS, 104: 20805 (2007) [1]). It involves the translocation of charged residues across the hydrophobic core of the membrane and the passive diffusion of these highly charged peptides across the membrane through the formation of aqueous toroidal pores. The aim of this review is to discuss the details of the mechanism and interpret some experimental results consistent with this view.
Language	English
Publishing date	2008-05-15
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2016734-9
ISSN	1573-0689 ; 0092-0606
ISSN (online)	1573-0689
ISSN	0092-0606
DOI	10.1007/s10867-008-9074-3
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Article ; Online: Structural basis for defective membrane targeting of mutant enzyme in human VLCAD deficiency

Michelle S. Prew / Christina M. Camara / Thomas Botzanowski / Jamie A. Moroco / Noah B. Bloch / Hannah R. Levy / Hyuk-Soo Seo / Sirano Dhe-Paganon / Gregory H. Bird / Henry D. Herce / Micah A. Gygi / Silvia Escudero / Thomas E. Wales / John R. Engen / Loren D. Walensky

Nature Communications, Vol 13, Iss 1, Pp 1-

2022 Volume 12

Abstract: Prew et al. uncovered a structural basis for human VLCAD deficiency that arises from point mutations within the enzyme’s membrane-binding region, which was shown to fold as a putative α-helical hairpin. Helix-breaking mutations selectively disrupt ... ...

Abstract	Prew et al. uncovered a structural basis for human VLCAD deficiency that arises from point mutations within the enzyme’s membrane-binding region, which was shown to fold as a putative α-helical hairpin. Helix-breaking mutations selectively disrupt membrane interaction and thus homeostatic function.
Keywords	Science ; Q
Language	English
Publishing date	2022-06-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
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Article ; Online: Molecular dynamics simulations suggest a mechanism for translocation of the HIV-1 TAT peptide across lipid membranes.

Herce, Henry D / Garcia, Angel E

Proceedings of the National Academy of Sciences of the United States of America

2007 Volume 104, Issue 52, Page(s) 20805–20810

Abstract: The recombinant HIV-1 Tat protein contains a small region corresponding to residues (47)YGRKKRRQRR(57)R, which is capable of translocating cargoes of different molecular sizes, such as proteins, DNA, RNA, or drugs, across the cell membrane in an ... ...

Abstract	The recombinant HIV-1 Tat protein contains a small region corresponding to residues (47)YGRKKRRQRR(57)R, which is capable of translocating cargoes of different molecular sizes, such as proteins, DNA, RNA, or drugs, across the cell membrane in an apparently energy-independent manner. The pathway that these peptides follow for entry into the cell has been the subject of strong controversy for the last decade. This peptide is highly basic and hydrophilic. Therefore, a central question that any candidate mechanism has to answer is how this highly hydrophilic peptide is able to cross the hydrophobic barrier imposed by the cell membrane. We propose a mechanism for the spontaneous translocation of the Tat peptides across a lipid membrane. This mechanism involves strong interactions between the Tat peptides and the phosphate groups on both sides of the lipid bilayer, the insertion of charged side chains that nucleate the formation of a transient pore, followed by the translocation of the Tat peptides by diffusing on the pore surface. This mechanism explains how key ingredients, such as the cooperativity among the peptides, the large positive charge, and specifically the arginine amino acids, contribute to the uptake. The proposed mechanism also illustrates the importance of membrane fluctuations. Indeed, mechanisms that involve large fluctuations of the membrane structure, such as transient pores and the insertion of charged amino acid side chains, may be common and perhaps central to the functions of many membrane protein functions.
MeSH term(s)	Amino Acids/chemistry ; Antimicrobial Cationic Peptides/chemistry ; Arginine/chemistry ; Cell Membrane/virology ; Computer Simulation ; Crystallography, X-Ray/methods ; Drug Delivery Systems ; Humans ; Lipid Bilayers/chemistry ; Lipids/chemistry ; Membrane Lipids/chemistry ; Microscopy, Confocal ; Molecular Conformation ; Peptides/chemistry ; Protein Conformation ; Water/chemistry ; tat Gene Products, Human Immunodeficiency Virus/chemistry
Chemical Substances	Amino Acids ; Antimicrobial Cationic Peptides ; Lipid Bilayers ; Lipids ; Membrane Lipids ; Peptides ; tat Gene Products, Human Immunodeficiency Virus ; Water (059QF0KO0R) ; Arginine (94ZLA3W45F)
Language	English
Publishing date	2007-12-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.0706574105
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Article: Correction of apparent finite size effects in the area per lipid of lipid membranes simulations.

Herce, Henry D / Garcia, Angel E

The Journal of chemical physics

2006 Volume 125, Issue 22, Page(s) 224711

Abstract: Molecular dynamics simulations of lipids bilayers have reported that the average area per lipid increases with the size of the simulated unit cell under constant temperature, pressure, and number of molecules. Here we show that the cause of this finite ... ...

Abstract	Molecular dynamics simulations of lipids bilayers have reported that the average area per lipid increases with the size of the simulated unit cell under constant temperature, pressure, and number of molecules. Here we show that the cause of this finite size effect are artifacts associated with the heat bath coupling. This can be corrected by coupling individually each degree of freedom to the heat bath, instead of coupling globally the system. We present the results of the investigation on three aspects of molecular dynamics simulations and their effect on the computed average area per lipid: (I) the accuracy in the computation of electrostatic interactions, the energy, and the virial, (II) long range Lennard-Jones interactions for systems with symmetry in one plane, and (III) thermodynamic baths. We show that the average area per lipid remains constant for simulations of systems containing 32, 64, and 256 lipids.
MeSH term(s)	Artifacts ; Computer Simulation ; Lipid Bilayers/chemistry ; Membrane Fluidity ; Models, Chemical ; Models, Molecular ; Particle Size
Chemical Substances	Lipid Bilayers
Language	English
Publishing date	2006-12-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/1.2378893
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