LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 7 of total 7

Search options

  1. Article: Stiff Spring Approximation Revisited: Inertial Effects in Nonequilibrium Trajectories

    Nategholeslam, Mostafa / Gray C. G / Tomberli Bruno

    Journal of physical chemistry. 2017 Jan. 19, v. 121, no. 2

    2017  

    Abstract: Use of harmonic guiding potentials is the most commonly adopted method for implementing steered molecular dynamics (SMD) simulations, performed to obtain potentials of mean force (PMFs) using Jarzynski’s equality and other nonequilibrium work (NEW) ... ...

    Abstract Use of harmonic guiding potentials is the most commonly adopted method for implementing steered molecular dynamics (SMD) simulations, performed to obtain potentials of mean force (PMFs) using Jarzynski’s equality and other nonequilibrium work (NEW) theorems. The stiff spring approximation (SSA) of Schulten and co-workers enables calculation of the PMF by using the work performed along many SMD trajectories in NEW theorems. We discuss and demonstrate how a high spring constant, k, required for the validity of the SSA can violate another requirement of SSA, the validity of Brownian dynamics in the system under study. These result in skewed work distributions with their width increasing with k. The skew and broadening of work distributions result in biased estimation (through invoking NEW theorems) of the PMF. Remarkably, the skewness and the broadening of work distributions are independent of the average drift velocity and physical asymmetries and can only be attributed to using too-stiff springs. We discuss the proper upper limit for k such that the inertial effects are minimized. In the presence of inertial effects, using the peak value (rather than the statistical mean) of the work distributions vastly reduces the bias in the calculated PMFs and improves the accuracy.
    Keywords molecular dynamics ; simulation models ; statistical analysis
    Language English
    Dates of publication 2017-0119
    Size p. 391-403.
    Publishing place American Chemical Society
    Document type Article
    ISSN 1520-5207
    DOI 10.1021%2Facs.jpcb.6b08701
    Database NAL-Catalogue (AGRICOLA)

    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: Stiff Spring Approximation Revisited: Inertial Effects in Nonequilibrium Trajectories.

    Nategholeslam, Mostafa / Gray, C G / Tomberli, Bruno

    The journal of physical chemistry. B

    2017  Volume 121, Issue 2, Page(s) 391–403

    Abstract: Use of harmonic guiding potentials is the most commonly adopted method for implementing steered molecular dynamics (SMD) simulations, performed to obtain potentials of mean force (PMFs) using Jarzynski's equality and other nonequilibrium work (NEW) ... ...

    Abstract Use of harmonic guiding potentials is the most commonly adopted method for implementing steered molecular dynamics (SMD) simulations, performed to obtain potentials of mean force (PMFs) using Jarzynski's equality and other nonequilibrium work (NEW) theorems. The stiff spring approximation (SSA) of Schulten and co-workers enables calculation of the PMF by using the work performed along many SMD trajectories in NEW theorems. We discuss and demonstrate how a high spring constant, k, required for the validity of the SSA can violate another requirement of SSA, the validity of Brownian dynamics in the system under study. These result in skewed work distributions with their width increasing with k. The skew and broadening of work distributions result in biased estimation (through invoking NEW theorems) of the PMF. Remarkably, the skewness and the broadening of work distributions are independent of the average drift velocity and physical asymmetries and can only be attributed to using too-stiff springs. We discuss the proper upper limit for k such that the inertial effects are minimized. In the presence of inertial effects, using the peak value (rather than the statistical mean) of the work distributions vastly reduces the bias in the calculated PMFs and improves the accuracy.
    Language English
    Publishing date 2017-01-19
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.6b08701
    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: Implementation of the Forward–Reverse Method for Calculating the Potential of Mean Force Using a Dynamic Restraining Protocol

    Nategholeslam, Mostafa / Gray C. G / Tomberli Bruno

    Journal of physical chemistry. 2014 Dec. 11, v. 118, no. 49

    2014  

    Abstract: We present a new sampling and analysis scheme for calculating the potential of mean force (PMF) of systems studied by steered molecular dynamics simulations. This scheme, which we call the bin-passing method, is based on the forward–reverse (FR) method ...

    Abstract We present a new sampling and analysis scheme for calculating the potential of mean force (PMF) of systems studied by steered molecular dynamics simulations. This scheme, which we call the bin-passing method, is based on the forward–reverse (FR) method (due to I. Kosztin and co-workers, Kosztin et al. J. Chem. Phys. 2006, 124(6), 064106) and arguments based on the second law of thermodynamics. Applying the bin-passing method results in enhanced sampling, better separation of the reversible and irreversible work distributions, and faster convergence to the underlying PMF of the system under study. Post-simulation analysis is performed using a purpose-built software that we have made publicly available at https://github.com/1particle/bin-passing_analyzer under the terms of the GNU General Public License (version 3). Three examples are provided, for systems of varying sizes and complexities, to demonstrate the efficiency of this method and the quality of the results: for the dissociation PMF of NaCl in water, the bin-passing method obtains PMFs in excellent agreement with that obtained for the same system and using the same force-field through static (equilibrium) methods. The bin-passing method gives a very symmetric PMF for passage of a single water molecule through a DPPC bilayer, and the resultant PMF leads to permeability values in better agreement with experiments than those obtained through previous simulation studies. Finally, we consider the interaction of the antimicrobial peptide HHC-36 with two model membranes and employ the bin-passing method to obtain the PMFs for peptide adsorption to the membranes. The characteristics of these PMFs are consistent with the qualities established for the HHC-36 peptide through in vivo and in vitro experiments, as a non-toxic strong antimicrobial agent.
    Keywords adsorption ; anti-infective agents ; antimicrobial peptides ; computer software ; dissociation ; in vitro studies ; models ; molecular dynamics ; permeability ; sodium chloride ; thermodynamics
    Language English
    Dates of publication 2014-1211
    Size p. 14203-14214.
    Publishing place American Chemical Society
    Document type Article
    ISSN 1520-5207
    DOI 10.1021%2Fjp504942t
    Database NAL-Catalogue (AGRICOLA)

    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.

  4. Article ; Online: Implementation of the forward-reverse method for calculating the potential of mean force using a dynamic restraining protocol.

    Nategholeslam, Mostafa / Gray, C G / Tomberli, Bruno

    The journal of physical chemistry. B

    2014  Volume 118, Issue 49, Page(s) 14203–14214

    Abstract: We present a new sampling and analysis scheme for calculating the potential of mean force (PMF) of systems studied by steered molecular dynamics simulations. This scheme, which we call the bin-passing method, is based on the forward-reverse (FR) method ( ... ...

    Abstract We present a new sampling and analysis scheme for calculating the potential of mean force (PMF) of systems studied by steered molecular dynamics simulations. This scheme, which we call the bin-passing method, is based on the forward-reverse (FR) method (due to I. Kosztin and co-workers, Kosztin et al. J. Chem. Phys. 2006, 124(6), 064106) and arguments based on the second law of thermodynamics. Applying the bin-passing method results in enhanced sampling, better separation of the reversible and irreversible work distributions, and faster convergence to the underlying PMF of the system under study. Post-simulation analysis is performed using a purpose-built software that we have made publicly available at https://github.com/1particle/bin-passing_analyzer under the terms of the GNU General Public License (version 3). Three examples are provided, for systems of varying sizes and complexities, to demonstrate the efficiency of this method and the quality of the results: for the dissociation PMF of NaCl in water, the bin-passing method obtains PMFs in excellent agreement with that obtained for the same system and using the same force-field through static (equilibrium) methods. The bin-passing method gives a very symmetric PMF for passage of a single water molecule through a DPPC bilayer, and the resultant PMF leads to permeability values in better agreement with experiments than those obtained through previous simulation studies. Finally, we consider the interaction of the antimicrobial peptide HHC-36 with two model membranes and employ the bin-passing method to obtain the PMFs for peptide adsorption to the membranes. The characteristics of these PMFs are consistent with the qualities established for the HHC-36 peptide through in vivo and in vitro experiments, as a non-toxic strong antimicrobial agent.
    Language English
    Publishing date 2014-12-11
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/jp504942t
    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. Book ; Online: Stiff-spring approximation revisited

    Nategholeslam, Mostafa / Gray, C. G. / Tomberli, Bruno

    inertial effects in non-equilibrium trajectories

    2016  

    Abstract: Use of harmonic guiding potentials is the most common method for implementing steered molecular dynamics (SMD) simulations, performed to obtain potentials of mean force (PMFs) of molecular systems using non-equilibrium work (NEW) theorems. Harmonic ... ...

    Abstract Use of harmonic guiding potentials is the most common method for implementing steered molecular dynamics (SMD) simulations, performed to obtain potentials of mean force (PMFs) of molecular systems using non-equilibrium work (NEW) theorems. Harmonic guiding potentials are also the natural choice in single molecule force spectroscopy experiments. The stiff spring approximation (SSA) of Schulten and coworkers enables to use the work performed along SMD trajectories to obtain the PMF. We discuss and demonstrate how a high spring constant, k, required for the validity of the SSA can violate another requirement of this theory, i.e., the validity of Brownian dynamics of the system. Violation of the Brownian condition results in the introduction of kinetic energy contributions to the external work, performed during SMD simulations. These inertial effects result in skewed work distributions, rather than the Gaussian distributions predicted by SSA. The inertial effects also result in broader work distributions, which worsen the effect of the skewness when calculating work averages. Remarkably, our results strongly suggest that the skew and width of work distributions are independent of the average drift velocity and physical asymmetries. The skew and broadening of work distributions result in biased estimation of the PMF. The bias manifests itself in the form of a systematic error that increases with simulation time. We discuss the proper upper limit for k, such that the inertial effects are avoided. This limit, used together with the relation for the lower limit of k, enables to conduct accurate steering while satisfying the Brownian dynamics. Furthermore, we argue and demonstrate that using the peak-value (rather than the statistical mean) of the work distributions vastly reduces the bias in the calculated PMFs and improves the accuracy.
    Keywords Physics - Computational Physics ; Condensed Matter - Statistical Mechanics ; Physics - Biological Physics
    Subject code 612
    Publishing date 2016-07-25
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    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: Dynamic Turn Conformation of a Short Tryptophan-Rich Cationic Antimicrobial Peptide and Its Interaction with Phospholipid Membranes

    Nichols, Matthew / Kuljanin Miljan / Nategholeslam Mostafa / Hoang Tuan / Vafaei Shaghayegh / Tomberli Bruno / Gray C. G / DeBruin Lillian / Jelokhani-Niaraki Masoud

    Journal of physical chemistry. 2013 Nov. 27, v. 117, no. 47

    2013  

    Abstract: Cationic antimicrobial peptides are promising sources for novel therapeutic agents against multi-drug-resistant bacteria. HHC-36 (KRWWKWWRR) is a simple but effective antimicrobial peptide with similar or superior activity compared with several ... ...

    Abstract Cationic antimicrobial peptides are promising sources for novel therapeutic agents against multi-drug-resistant bacteria. HHC-36 (KRWWKWWRR) is a simple but effective antimicrobial peptide with similar or superior activity compared with several conventional antibiotics. In this biophysical study, unique conformational properties of this peptide and some of its analogs as well as its interaction with lipid membranes are investigated in detail. Circular dichroism (CD) and molecular dynamics modeling studies of HHC-36 in different environments reveal a dynamic amphipathic structure composed of competing turn conformations with free energies lower than that of the unfolded state, implying a strong influence of tryptophan interactions in formation of the turns. CD spectra and gel electrophoresis also show strong evidence of self-association of this peptide in aqueous milieu and interaction with both neutrally and negatively charged lipid membrane systems. Isothermal titration calorimetry and acrylamide fluorescence quenching experiments emphasize the preference of HHC-36 for negatively charged vesicles. In addition, dye leakage experiments suggest that this peptide functions through a surface-associated mechanism with weak lytic activity against bacterial model membranes.
    Keywords acrylamides ; antibiotics ; antimicrobial peptides ; bacteria ; calorimetry ; circular dichroism spectroscopy ; fluorescence ; gel electrophoresis ; models ; molecular dynamics ; multiple drug resistance ; phospholipids ; titration ; tryptophan
    Language English
    Dates of publication 2013-1127
    Size p. 14697-14708.
    Publishing place American Chemical Society
    Document type Article
    ISSN 1520-5207
    DOI 10.1021%2Fjp4096985
    Database NAL-Catalogue (AGRICOLA)

    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: Dynamic turn conformation of a short tryptophan-rich cationic antimicrobial peptide and its interaction with phospholipid membranes.

    Nichols, Matthew / Kuljanin, Miljan / Nategholeslam, Mostafa / Hoang, Tuan / Vafaei, Shaghayegh / Tomberli, Bruno / Gray, C G / DeBruin, Lillian / Jelokhani-Niaraki, Masoud

    The journal of physical chemistry. B

    2013  Volume 117, Issue 47, Page(s) 14697–14708

    Abstract: Cationic antimicrobial peptides are promising sources for novel therapeutic agents against multi-drug-resistant bacteria. HHC-36 (KRWWKWWRR) is a simple but effective antimicrobial peptide with similar or superior activity compared with several ... ...

    Abstract Cationic antimicrobial peptides are promising sources for novel therapeutic agents against multi-drug-resistant bacteria. HHC-36 (KRWWKWWRR) is a simple but effective antimicrobial peptide with similar or superior activity compared with several conventional antibiotics. In this biophysical study, unique conformational properties of this peptide and some of its analogs as well as its interaction with lipid membranes are investigated in detail. Circular dichroism (CD) and molecular dynamics modeling studies of HHC-36 in different environments reveal a dynamic amphipathic structure composed of competing turn conformations with free energies lower than that of the unfolded state, implying a strong influence of tryptophan interactions in formation of the turns. CD spectra and gel electrophoresis also show strong evidence of self-association of this peptide in aqueous milieu and interaction with both neutrally and negatively charged lipid membrane systems. Isothermal titration calorimetry and acrylamide fluorescence quenching experiments emphasize the preference of HHC-36 for negatively charged vesicles. In addition, dye leakage experiments suggest that this peptide functions through a surface-associated mechanism with weak lytic activity against bacterial model membranes.
    MeSH term(s) Amino Acid Sequence ; Anti-Infective Agents/chemistry ; Anti-Infective Agents/pharmacology ; Antimicrobial Cationic Peptides/chemistry ; Antimicrobial Cationic Peptides/pharmacology ; Circular Dichroism ; Lipid Bilayers/metabolism ; Molecular Dynamics Simulation ; Phospholipids/metabolism ; Protein Structure, Secondary ; Tryptophan/chemistry ; Tryptophan/pharmacology
    Chemical Substances Anti-Infective Agents ; Antimicrobial Cationic Peptides ; Lipid Bilayers ; Phospholipids ; Tryptophan (8DUH1N11BX)
    Language English
    Publishing date 2013-11-27
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/jp4096985
    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.

To top