IDEAS home Printed from https://ideas.repec.org/a/eee/phsmap/v644y2024ics0378437124003534.html
   My bibliography  Save this article

Calculating structure factors of protein solutions by atomistic modeling of protein-protein interactions

Author

Listed:
  • Qin, Sanbo
  • Zhou, Huan-Xiang

Abstract

We present a method, FMAPS(q), for calculating the structure factor, S(q), of a protein solution, by extending our fast Fourier transform-based modeling of atomistic protein-protein interactions (FMAP) approach. The interaction energy consists of steric, nonpolar attractive, and electrostatic terms that are additive among all pairs of atoms between two protein molecules. In the present version, we invoke the free-rotation approximation, such that the structure factor is given by the Fourier transform of the protein center-center distribution function gC(R). At low protein concentrations, gC(R) can be approximated as e−βW(R), where W(R) is the potential of mean force along the center-center distance R. We calculate W(R) using FMAPB2, a member of the FMAP class of methods that is specialized for the second virial coefficient [Qin and Zhou, J Phys Chem B 123 (2019) 8203–8215]. For higher protein concentrations, we obtain S(q) by a modified random-phase approximation, which is a perturbation around the steric-only energy function. Without adjusting any parameters, the calculated structure factors for lysozyme and bovine serum albumin at various ionic strengths, temperatures, and protein concentrations are all in reasonable agreement with those measured by small-angle X-ray or neutron scattering. This initial success motivates further developments, including removing approximations and parameterizing the interaction energy function.

Suggested Citation

  • Qin, Sanbo & Zhou, Huan-Xiang, 2024. "Calculating structure factors of protein solutions by atomistic modeling of protein-protein interactions," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 644(C).
  • Handle: RePEc:eee:phsmap:v:644:y:2024:i:c:s0378437124003534
    DOI: 10.1016/j.physa.2024.129844
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0378437124003534
    Download Restriction: Full text for ScienceDirect subscribers only. Journal offers the option of making the article available online on Science direct for a fee of $3,000

    File URL: https://libkey.io/10.1016/j.physa.2024.129844?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Anna Stradner & Helen Sedgwick & Frédéric Cardinaux & Wilson C. K. Poon & Stefan U. Egelhaaf & Peter Schurtenberger, 2004. "Equilibrium cluster formation in concentrated protein solutions and colloids," Nature, Nature, vol. 432(7016), pages 492-495, November.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Ian W. Hamley & Anindyasundar Adak & Valeria Castelletto, 2024. "Influence of chirality and sequence in lysine-rich lipopeptide biosurfactants and micellar model colloid systems," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    2. Alireza Hooshanginejad & Jack-William Barotta & Victoria Spradlin & Giuseppe Pucci & Robert Hunt & Daniel M. Harris, 2024. "Interactions and pattern formation in a macroscopic magnetocapillary SALR system of mermaid cereal," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
    3. Chi Zhang & José Muñetón Díaz & Augustin Muster & Diego R. Abujetas & Luis S. Froufe-Pérez & Frank Scheffold, 2024. "Determining intrinsic potentials and validating optical binding forces between colloidal particles using optical tweezers," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
    4. Emmanuel Stiakakis & Niklas Jung & Nataša Adžić & Taras Balandin & Emmanuel Kentzinger & Ulrich Rücker & Ralf Biehl & Jan K. G. Dhont & Ulrich Jonas & Christos N. Likos, 2021. "Self assembling cluster crystals from DNA based dendritic nanostructures," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
    5. Sondra S. Teske & Corrella S. Detweiler, 2015. "The Biomechanisms of Metal and Metal-Oxide Nanoparticles’ Interactions with Cells," IJERPH, MDPI, vol. 12(2), pages 1-23, January.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:eee:phsmap:v:644:y:2024:i:c:s0378437124003534. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Catherine Liu (email available below). General contact details of provider: http://www.journals.elsevier.com/physica-a-statistical-mechpplications/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.