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  1. Article ; Online: On the possibility of the existence of orienting hydrodynamic steering effects in the kinetics of receptor-ligand association.

    Antosiewicz, Jan M

    European biophysics journal : EBJ

    2023  Volume 52, Issue 6-7, Page(s) 559–568

    Abstract: In the vast majority of biologically relevant cases of receptor-ligand complex formation, the binding site of the receptor is a small part of its surface, and moreover, formation of a biologically active complex often requires a specific orientation of ... ...

    Abstract In the vast majority of biologically relevant cases of receptor-ligand complex formation, the binding site of the receptor is a small part of its surface, and moreover, formation of a biologically active complex often requires a specific orientation of the ligand relative to the binding site. Before the formation of the initial form of the complex, only long-range, electrostatic and hydrodynamic interactions can act between the ligand approaching the binding site and the receptor. In this context, the question arises whether as a result of these interactions, there is a pre-orientation of the ligand towards the binding site, which to some extent would accelerate the formation of the complex. The role of electrostatic interactions in the orientation of the ligand relative to the binding site of the receptor is well documented. The analogous role of hydrodynamic interactions, although assessed as very significant by Brune and Kim (PNAS 91, 2930-2934, (1994)), is still debatable. In this article, I present the current state of knowledge on this subject and consider the possibilities of demonstrating the orienting effect of hydrodynamic interactions in the processes of receptor-ligand association, in an experimental way supported by computer simulations.
    MeSH term(s) Ligands ; Hydrodynamics ; Diffusion ; Protein Binding ; Computer Simulation ; Kinetics ; Carrier Proteins
    Chemical Substances Ligands ; Carrier Proteins
    Language English
    Publishing date 2023-05-12
    Publishing country Germany
    Document type Journal Article ; Review
    ZDB-ID 283671-3
    ISSN 1432-1017 ; 0175-7571
    ISSN (online) 1432-1017
    ISSN 0175-7571
    DOI 10.1007/s00249-023-01653-0
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    Zs.A 1121: Show issues Location:
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  2. Article: Editorial: Intracellular Molecular Processes Affected by pH.

    Antosiewicz, Jan M / Kane, Patricia M

    Frontiers in molecular biosciences

    2022  Volume 9, Page(s) 891533

    Language English
    Publishing date 2022-04-11
    Publishing country Switzerland
    Document type Editorial
    ZDB-ID 2814330-9
    ISSN 2296-889X
    ISSN 2296-889X
    DOI 10.3389/fmolb.2022.891533
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  3. Article ; Online: Special Issue: 18th Congress of the Polish Biophysical Society.

    Antosiewicz, Jan M / Gilbert, Robert / Marszalek, Piotr E

    European biophysics journal : EBJ

    2023  Volume 52, Issue 6-7, Page(s) 483–486

    Abstract: The 18th Congress of the Polish Biophysical Society took place at the Faculty of Physics of the University of Warsaw in Warsaw, Poland, in September 2022. In total, 111 attendees (Attendance Profile: 107 in-person, 4 remote; Italy 1, Lithuania 1, Poland ... ...

    Abstract The 18th Congress of the Polish Biophysical Society took place at the Faculty of Physics of the University of Warsaw in Warsaw, Poland, in September 2022. In total, 111 attendees (Attendance Profile: 107 in-person, 4 remote; Italy 1, Lithuania 1, Poland 104, United Kingdom 1, United States 4) participated in the event. The authors of lectures and posters at the Congress were invited to prepare their presentations in the form of articles in this special issue of the European Biophysics Journal. The 11 articles published in this special issue present a limited sampling of the subjects of the conference presentations. Nevertheless, they showcase excellence in Polish biophysics across a wide range of topics, using both theoretical and experimental approaches: mechanisms of receptor-ligand interactions, medical applications of proteins and nucleic acids, non-linear dynamics/molecular dynamics of protein systems, hydrodynamics and biosensing. We hope to improve on the representation of the international Polish biophysical community after the next Congress in 2025.
    MeSH term(s) Humans ; Poland ; Italy ; Biophysics
    Language English
    Publishing date 2023-10-26
    Publishing country Germany
    Document type Editorial
    ZDB-ID 283671-3
    ISSN 1432-1017 ; 0175-7571
    ISSN (online) 1432-1017
    ISSN 0175-7571
    DOI 10.1007/s00249-023-01688-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1121: 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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  4. Article ; Online: Kinetics of Structural Transitions Induced by Sodium Dodecyl Sulfate in α-Chymotrypsin.

    Stachurska, Karolina / Marcisz, Urszula / Długosz, Maciej / Antosiewicz, Jan M

    ACS omega

    2023  Volume 8, Issue 51, Page(s) 49137–49149

    Abstract: The temporal changes in circular dichroism at 222 and 260 nm were recorded by using stopped-flow spectroscopy after mixing α-chymotrypsin solutions with sodium dodecyl sulfate solutions. Simultaneously with the circular dichroism signal, the fluorescence ...

    Abstract The temporal changes in circular dichroism at 222 and 260 nm were recorded by using stopped-flow spectroscopy after mixing α-chymotrypsin solutions with sodium dodecyl sulfate solutions. Simultaneously with the circular dichroism signal, the fluorescence emission was recorded. Changes in the secondary and tertiary structures of chymotrypsin induced by sodium dodecyl sulfate are characterized by either three or four one-way reactions with relaxation amplitudes and times precisely determined by an advanced numerical procedure of Kuzmič. Quantitatively, transitions within the secondary and tertiary structures of the protein are significantly different. Moreover, changes in the tertiary structure depend on the type of recorded signal (either circular dichroism or fluorescence) and the wavelength of the incident radiation. The latter observation is particularly interesting as it indicates that the contributions of protein's different tryptophans to the total recorded fluorescence depend on the excitation wavelength. We present several results justifying this hypothesis.
    Language English
    Publishing date 2023-12-13
    Publishing country United States
    Document type Journal Article
    ISSN 2470-1343
    ISSN (online) 2470-1343
    DOI 10.1021/acsomega.3c07256
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  5. Article ; Online: Constant-pH Brownian Dynamics Simulations of a Protein near a Charged Surface.

    Antosiewicz, Jan M / Długosz, Maciej

    ACS omega

    2020  Volume 5, Issue 46, Page(s) 30282–30298

    Abstract: We have developed a rigid-body Brownian dynamics algorithm that allows for simulations of a globular protein suspended in an ionic solution confined by a charged planar boundary, with an explicit treatment of pH-dependent protein protonation equilibria ... ...

    Abstract We have developed a rigid-body Brownian dynamics algorithm that allows for simulations of a globular protein suspended in an ionic solution confined by a charged planar boundary, with an explicit treatment of pH-dependent protein protonation equilibria and their couplings to the electrostatic potential of the plane. Electrostatic interactions are described within a framework of the continuum Poisson-Boltzmann model, whereas protein-plane hydrodynamic interactions are evaluated based on analytical expressions for the position- and orientation-dependent near-wall friction tensor of a spheroid. The algorithm was applied to simulate near-surface diffusion of lysozyme in solutions having pH in the range 4-10 and ionic strengths of 10 and 150 mM. As a reference, we performed Brownian dynamics simulations in which the protein is assigned a fixed, most probable protonation state, appropriate for given solution conditions and unaffected by the presence of the charged plane, and Brownian dynamics simulations in which the protein probes possible protonation states with the pH-dependent probability, but these variations are not coupled to the electric field generated by the boundary. We show that electrostatic interactions with the negatively charged plane substantially modify probabilities of different protonation states of lysozyme and shift protonation equilibria of both acidic and basic amino acid side chains toward higher pH values. Consequently, equilibrium energy distributions, equilibrium position-orientation distributions, and functions that characterize rotational dynamics, which for a protein with multiple ionization sites, such as lysozyme, in the presence of a charged obstacle are pH-dependent, are significantly affected by the approach taken to incorporate the solution pH into simulations.
    Language English
    Publishing date 2020-11-12
    Publishing country United States
    Document type Journal Article
    ISSN 2470-1343
    ISSN (online) 2470-1343
    DOI 10.1021/acsomega.0c04817
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Editorial

    Jan M. Antosiewicz / Patricia M. Kane

    Frontiers in Molecular Biosciences, Vol

    Intracellular Molecular Processes Affected by pH

    2022  Volume 9

    Keywords protons and pH inside cells ; modelling molecular pH sensing ; maintaince of cellular pH ; pH dependent intracellular protein localization ; mechanisms of pH dependence of viral infection ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2022-04-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Searching for Hydrodynamic Orienting Effects in the Association of Tri-

    Wielgus-Kutrowska, Beata / Marcisz, Urszula / Antosiewicz, Jan M

    The journal of physical chemistry. B

    2021  Volume 125, Issue 38, Page(s) 10701–10709

    Abstract: Using stopped-flow fluorometry, we determined rate constants for the formation of diffusional encounter complexes of tri- ...

    Abstract Using stopped-flow fluorometry, we determined rate constants for the formation of diffusional encounter complexes of tri-
    MeSH term(s) Acetylglucosamine ; Animals ; Chickens/metabolism ; Hydrodynamics ; Muramidase/metabolism ; Osmolar Concentration ; Protein Binding
    Chemical Substances Muramidase (EC 3.2.1.17) ; Acetylglucosamine (V956696549)
    Language English
    Publishing date 2021-09-21
    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/acs.jpcb.1c06762
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Constant-pH Brownian Dynamics Simulations of a Protein near a Charged Surface

    Jan M. Antosiewicz / Maciej Długosz

    ACS Omega, Vol 5, Iss 46, Pp 30282-

    2020  Volume 30298

    Keywords Chemistry ; QD1-999
    Language English
    Publishing date 2020-11-01T00:00:00Z
    Publisher American Chemical Society
    Document type Article ; Online
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  9. Article ; Online: Circular Dichroism Spectra of α-Chymotrypsin-SDS Solutions Depend on the Procedure of Their Preparation.

    Stachurska, Karolina / Marcisz, Urszula / Długosz, Maciej / Antosiewicz, Jan M

    ACS omega

    2022  Volume 7, Issue 27, Page(s) 23782–23789

    Abstract: We recorded the far- and near-UV circular dichroism (CD) spectra of solutions of α-chymotrypsin and sodium dodecyl sulfate (SDS) with the final surfactant concentration significantly above the critical micellization concentration. Solutions were prepared ...

    Abstract We recorded the far- and near-UV circular dichroism (CD) spectra of solutions of α-chymotrypsin and sodium dodecyl sulfate (SDS) with the final surfactant concentration significantly above the critical micellization concentration. Solutions were prepared using three different procedures. The reference procedure was to mix the chymotrypsin solution with the SDS solution once, immediately achieving the final SDS concentration. In alternative procedures, the protein solutions initially contained some SDS and were mixed with pure SDS solutions at a concentration to provide the same final surfactant as the reference mixing. We demonstrate that the supplementation to the selected final concentration of SDS of the pure chymotrypsin solution leads to different CD spectra than the supplementation to this final concentration of SDS in the chymotrypsin solution containing a small concentration of a few millimolar SDS. These differences disappear when the initial concentration of SDS in the protein solution, which we then supplement to the indicated final concentration, is higher. This suggests the irreversibility of the processes caused by the addition of SDS to chymotrypsin and the influence of the initial amount of this surfactant on the processes occurring with its further addition to the solution. For quantitative analysis of far-UV CD spectra in terms of populations of protein secondary structure elements, we used four well-established software packages. All programs consistently indicate that the observed differences in the far-UV CD spectra can be explained by the differences in the increase in the population of helical forms in chymotrypsin under the influence of SDS.
    Language English
    Publishing date 2022-06-28
    Publishing country United States
    Document type Journal Article
    ISSN 2470-1343
    ISSN (online) 2470-1343
    DOI 10.1021/acsomega.2c02438
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Does Ionic Screening Lower Activation Barriers for Conformational Transitions in Proteins?

    Antosiewicz, Jan M / Długosz, Maciej

    The journal of physical chemistry. B

    2018  Volume 122, Issue 50, Page(s) 11817–11826

    Abstract: In this work, we investigated the kinetics of binding of hen egg-white lysozyme with tri- N-acetylglucosamine in aqueous solutions, at two values of pH, 3.2 and 11, as a function of ionic strength, by a stopped-flow method with tryptophyl fluorescence ... ...

    Abstract In this work, we investigated the kinetics of binding of hen egg-white lysozyme with tri- N-acetylglucosamine in aqueous solutions, at two values of pH, 3.2 and 11, as a function of ionic strength, by a stopped-flow method with tryptophyl fluorescence observation of the transients. We analyzed registered reaction progress curves by employing numerical integration of appropriate chemical master equations. We discriminated between several binding models and established that the process observed in experiments follows a two-step mechanism, composed of four elementary stages: diffusional formation of an encounter complex, dissociation of the encounter complex, conformational transition of the encounter complex to the final complex, and the reverse transformation, i.e., from the final complex to the encounter complex. We evaluated rate constants of these elementary stages and determined their dependencies on solution ionic strength. Regardless of solution pH, rate constants of both forward and reverse conformational transitions increase with an increasing ionic strength. This suggests that ionic screening of intramolecular electrostatic interactions may act to lower the activation barrier for conformational transition in proteins.
    MeSH term(s) Hydrogen-Ion Concentration ; Ions/chemistry ; Kinetics ; Muramidase/chemistry ; Muramidase/metabolism ; Protein Conformation ; Trisaccharides/chemistry
    Chemical Substances Ions ; Trisaccharides ; N,N',N''-triacetylchitotriose (38864-21-0) ; hen egg lysozyme (EC 3.2.1.-) ; Muramidase (EC 3.2.1.17)
    Language English
    Publishing date 2018-12-07
    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/acs.jpcb.8b07525
    Database MEDical Literature Analysis and Retrieval System OnLINE

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