LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 10 of total 165

Search options

  1. Article ; Online: Defect Formation and Peptide Permeation across Phospholipid Membranes.

    Elber, Ron

    The journal of physical chemistry. B

    2023  Volume 127, Issue 37, Page(s) 7810–7818

    Abstract: Cell penetrating peptides (CPPs) are natural agents that efficiently permeate biological membranes. They are frequently positively charged, which is surprising since membranes pose hydrophobic barriers. In this Perspective, I discuss computations and ... ...

    Abstract Cell penetrating peptides (CPPs) are natural agents that efficiently permeate biological membranes. They are frequently positively charged, which is surprising since membranes pose hydrophobic barriers. In this Perspective, I discuss computations and experiments of a permeation model that couples permeant displacement with a membrane defect. We call the proposed mechanism Defect Assisted by Charge (DAC) and illustrate that it reduces the free energy barrier for translocation. A metastable state at the center of the membrane may be observed due to the charge interactions with the phospholipid head groups at the two leaflets. The combination of experiments and simulations sheds light on the mechanisms of a charged peptide translocation across phospholipid membranes.
    MeSH term(s) Membranes ; Cell Membrane ; Cell-Penetrating Peptides ; Phospholipids
    Chemical Substances Cell-Penetrating Peptides ; Phospholipids
    Language English
    Publishing date 2023-09-07
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.3c04895
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  2. Article ; Online: Comparison of Accuracy and Efficiency of Milestoning Variants: Introducing Buffer Milestoning.

    Narayan, Brajesh / Elber, Ron

    The journal of physical chemistry. B

    2024  Volume 128, Issue 6, Page(s) 1438–1447

    Abstract: The Milestoning algorithm is a method for long-time molecular dynamics simulations. It enables the sampling of rare events. The precise calculations of observables depend on accurately determining the first hitting point distribution (FHPD) for each ... ...

    Abstract The Milestoning algorithm is a method for long-time molecular dynamics simulations. It enables the sampling of rare events. The precise calculations of observables depend on accurately determining the first hitting point distribution (FHPD) for each milestone. There is no analytical expression for FHPD, which is estimated numerically. Several variants of Milestoning offer approximations to the FHPD. Here, we examine in detail the FHPD of an exact calculation and Milestoning variants. We also introduce a new version of the Milestoning algorithm, buffer Milestoning, with a comparable cost to conventional Milestoning but higher accuracy. We use the mean first passage time and the free energy to assess the simulation quality, and we compare the accuracy and efficiency of buffer Milestoning to exact calculations, conventional Milestoning, local-passage-time-weighted Milestoning, Markovian Milestoning with Voronoi tessellation, and exact Milestoning. Conventional Milestoning requires milestone decorrelation. If this condition is not satisfied, it is the least accurate approach of all the techniques we examined. We conclude that for a small increase in cost compared to conventional Milestoning, buffer Milestoning provides accurate results for a range of problems, including more correlated milestones and is, therefore, versatile compared to other variants. Local-passage-time-weighted Milestoning provides accuracy similar to that of buffer Milestoning but at an increased simulation cost. Markovian Milestoning with Voronoi tessellation is the most accurate compared with other approximations, but it is less stable for high barriers and more expensive.
    Language English
    Publishing date 2024-02-05
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.3c07933
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  3. Article ; Online: Milestoning: An Efficient Approach for Atomically Detailed Simulations of Kinetics in Biophysics.

    Elber, Ron

    Annual review of biophysics

    2020  Volume 49, Page(s) 69–85

    Abstract: Recent advances in theory and algorithms for atomically detailed simulations open the way to the study of the kinetics of a wide range of molecular processes in biophysics. The theories propose a shift from the traditionally very long molecular dynamic ... ...

    Abstract Recent advances in theory and algorithms for atomically detailed simulations open the way to the study of the kinetics of a wide range of molecular processes in biophysics. The theories propose a shift from the traditionally very long molecular dynamic trajectories, which are exact but may not be efficient in the study of kinetics, to the use of a large number of short trajectories. The short trajectories exploit a mapping to a mesh in coarse space and allow for efficient calculations of kinetics and thermodynamics. In this review, I focus on one theory: Milestoning is a theory and an algorithm that offers a hierarchical calculation of properties of interest, such as the free energy profile and the mean first passage time. Approximations to the true long-time dynamics can be computed efficiently and assessed at different steps of the investigation. The theory is discussed and illustrated using two biophysical examples: ion permeation through a phospholipid membrane and protein translocation through a channel.
    MeSH term(s) Algorithms ; Biophysical Phenomena ; Kinetics ; Models, Biological ; Thermodynamics
    Language English
    Publishing date 2020-05-11
    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. ; Review
    ZDB-ID 2434725-5
    ISSN 1936-1238 ; 1936-122X
    ISSN (online) 1936-1238
    ISSN 1936-122X
    DOI 10.1146/annurev-biophys-121219-081528
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Se 190: 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)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  4. Article ; Online: Correction to "Simple and Analytical Model of RNA Collapse".

    Templeton, Clark / Elber, Ron

    The journal of physical chemistry. B

    2021  Volume 125, Issue 27, Page(s) 7573–7574

    Language English
    Publishing date 2021-06-30
    Publishing country United States
    Document type Published Erratum
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.1c05103
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  5. Article ; Online: Impact of Ion-Mixing Entropy on Orientational Preferences of DNA Helices: FRET Measurements and Computer Simulations.

    Templeton, Clark / Hamilton, Ian / Russell, Rick / Elber, Ron

    The journal of physical chemistry. B

    2023  Volume 127, Issue 41, Page(s) 8796–8808

    Abstract: Biological processes require DNA and RNA helices to pack together in specific interhelical orientations. While electrostatic repulsion between backbone charges is expected to be maximized when helices are in parallel alignment, such orientations are ... ...

    Abstract Biological processes require DNA and RNA helices to pack together in specific interhelical orientations. While electrostatic repulsion between backbone charges is expected to be maximized when helices are in parallel alignment, such orientations are commonplace in nature. To better understand how the repulsion is overcome, we used experimental and computational approaches to investigate how the orientational preferences of DNA helices depend on the concentration and valence of mobile cations. We used Förster resonance energy transfer (FRET) to probe the relative orientations of two 24-bp helices held together via a freely rotating PEG linker. At low cation concentrations, the helices preferred more "cross"-like orientations over those closer to parallel, and this preference was reduced with increasing salt concentrations. The results were in good quantitative agreement with Poisson-Boltzmann (PB) calculations for monovalent salt (Na
    MeSH term(s) Fluorescence Resonance Energy Transfer ; Entropy ; Nucleic Acid Conformation ; DNA/metabolism ; Molecular Dynamics Simulation ; Cations ; Sodium ; Sodium Chloride ; Static Electricity
    Chemical Substances DNA (9007-49-2) ; Cations ; Sodium (9NEZ333N27) ; Sodium Chloride (451W47IQ8X)
    Language English
    Publishing date 2023-10-10
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.3c04354
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  6. Article ; Online: Approximating First Hitting Point Distribution in Milestoning for Rare Event Kinetics.

    Wang, Ru / Wang, Hao / Liu, Wenjian / Elber, Ron

    Journal of chemical theory and computation

    2023  Volume 19, Issue 19, Page(s) 6816–6826

    Abstract: Milestoning is an efficient method for rare event kinetics calculation using short trajectory parallelization. Mean first passage time (MFPT) is the key kinetic output of Milestoning, whose accuracy crucially depends on the initial distribution of the ... ...

    Abstract Milestoning is an efficient method for rare event kinetics calculation using short trajectory parallelization. Mean first passage time (MFPT) is the key kinetic output of Milestoning, whose accuracy crucially depends on the initial distribution of the short trajectory ensemble. The true initial distribution, i.e., the first hitting point distribution (FHPD), has no analytic expression in the general case. Here, we introduce two algorithms, local passage time weighted Milestoning (LPT-M) and Bayesian inference Milestoning (BI-M), to accurately and efficiently approximate FHPD for systems at equilibrium condition. Starting from sampling the Boltzmann distribution on milestones, we calculate the proper weighting factor for the short trajectory ensemble. The methods are tested on two model examples for illustration purpose. Both methods improve significantly over the widely used classical Milestoning (CM) method in terms of the accuracy of MFPT. In particular, BI-M covers the directional Milestoning method as a special case in deterministic Hamiltonian dynamics. LPT-M is especially advantageous in terms of computational costs and robustness with respect to the increasing number of intermediate milestones. Furthermore, a locally iterative correction algorithm for nonequilibrium stationary FHPD is developed for exact MFPT calculation, which can be combined with LPT-M/BI-M and is much cheaper than the exact Milestoning (ExM) method.
    Language English
    Publishing date 2023-09-11
    Publishing country United States
    Document type Journal Article
    ISSN 1549-9626
    ISSN (online) 1549-9626
    DOI 10.1021/acs.jctc.3c00315
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  7. Article ; Online: A new paradigm for atomically detailed simulations of kinetics in biophysical systems.

    Elber, Ron

    Quarterly reviews of biophysics

    2017  Volume 50, Page(s) e8

    Abstract: The kinetics of biochemical and biophysical events determined the course of life processes and attracted considerable interest and research. For example, modeling of biological networks and cellular responses relies on the availability of information on ... ...

    Abstract The kinetics of biochemical and biophysical events determined the course of life processes and attracted considerable interest and research. For example, modeling of biological networks and cellular responses relies on the availability of information on rate coefficients. Atomically detailed simulations hold the promise of supplementing experimental data to obtain a more complete kinetic picture. However, simulations at biological time scales are challenging. Typical computer resources are insufficient to provide the ensemble of trajectories at the correct length that is required for straightforward calculations of time scales. In the last years, new technologies emerged that make atomically detailed simulations of rate coefficients possible. Instead of computing complete trajectories from reactants to products, these approaches launch a large number of short trajectories at different positions. Since the trajectories are short, they are computed trivially in parallel on modern computer architecture. The starting and termination positions of the short trajectories are chosen, following statistical mechanics theory, to enhance efficiency. These trajectories are analyzed. The analysis produces accurate estimates of time scales as long as hours. The theory of Milestoning that exploits the use of short trajectories is discussed, and several applications are described.
    MeSH term(s) Biophysics/methods ; Kinetics ; Models, Molecular
    Language English
    Publishing date 2017
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 209912-3
    ISSN 1469-8994 ; 0033-5835
    ISSN (online) 1469-8994
    ISSN 0033-5835
    DOI 10.1017/S0033583517000063
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.B 387: 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)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  8. Article: The Structures of Heterogeneous Membranes and Their Interactions with an Anticancer Peptide: A Molecular Dynamics Study.

    Abbas, Ghulam / Cardenas, Alfredo E / Elber, Ron

    Life (Basel, Switzerland)

    2022  Volume 12, Issue 10

    Abstract: We conduct molecular dynamics simulations of model heterogeneous membranes and their interactions with a 24-amino acid peptide-NAF- ... ...

    Abstract We conduct molecular dynamics simulations of model heterogeneous membranes and their interactions with a 24-amino acid peptide-NAF-1
    Language English
    Publishing date 2022-09-22
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2662250-6
    ISSN 2075-1729
    ISSN 2075-1729
    DOI 10.3390/life12101473
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  9. Article ; Online: Catalytic Magnesium as a Door Stop for DNA Sliding.

    Wang, Hao / Elber, Ron

    The journal of physical chemistry. B

    2021  Volume 125, Issue 14, Page(s) 3494–3500

    Abstract: The protein HIV Reverse Transcriptase (HIV RT) synthesizes a DNA strand according to a template. During the synthesis, the polymerase slides on the double stranded DNA to allow the entry of a new nucleotide to the active site. We use Molecular Dynamics ... ...

    Abstract The protein HIV Reverse Transcriptase (HIV RT) synthesizes a DNA strand according to a template. During the synthesis, the polymerase slides on the double stranded DNA to allow the entry of a new nucleotide to the active site. We use Molecular Dynamics simulations to estimate the free energy profile and the time scale of the DNA-protein's relative displacement in the complex's closed state. We illustrate that the presence of the catalytic magnesium slows down the process. Upon removing the catalytic magnesium ion, the process is rapid and significantly faster than reopening the active site in preparation for the new substrate. We speculate that magnesium regulates DNA translocation. The magnesium locks the DNA into a specific orientation during the chemical addition of the nucleotide. The release of Mg
    MeSH term(s) Catalytic Domain ; DNA ; DNA, Viral ; HIV Reverse Transcriptase/genetics ; HIV Reverse Transcriptase/metabolism ; Magnesium ; Nucleotides
    Chemical Substances DNA, Viral ; Nucleotides ; DNA (9007-49-2) ; HIV Reverse Transcriptase (EC 2.7.7.49) ; Magnesium (I38ZP9992A)
    Language English
    Publishing date 2021-04-05
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.1c00122
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  10. Article ; Online: Perspective: Computer simulations of long time dynamics.

    Elber, Ron

    The Journal of chemical physics

    2016  Volume 144, Issue 6, Page(s) 60901

    Abstract: Atomically detailed computer simulations of complex molecular events attracted the imagination of many researchers in the field as providing comprehensive information on chemical, biological, and physical processes. However, one of the greatest ... ...

    Abstract Atomically detailed computer simulations of complex molecular events attracted the imagination of many researchers in the field as providing comprehensive information on chemical, biological, and physical processes. However, one of the greatest limitations of these simulations is of time scales. The physical time scales accessible to straightforward simulations are too short to address many interesting and important molecular events. In the last decade significant advances were made in different directions (theory, software, and hardware) that significantly expand the capabilities and accuracies of these techniques. This perspective describes and critically examines some of these advances.
    MeSH term(s) Kinetics ; Molecular Dynamics Simulation
    Language English
    Publishing date 2016-02-14
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 3113-6
    ISSN 1089-7690 ; 0021-9606
    ISSN (online) 1089-7690
    ISSN 0021-9606
    DOI 10.1063/1.4940794
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

    More links

    Kategorien

    In stock of ZB MED Bonn / Germany

    Z 4' 49/16: Show issues

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

To top