Instytut Podstawowych Problemów Techniki
Polskiej Akademii Nauk

Partnerzy

Mateusz Chwastyk

Institute of Physics, Polish Academy of Sciences (PL)

Ostatnie publikacje
1.  Cofas Vargas L.F., Azevedo Rodrigo M., Poblete S., Chwastyk M., Poma Bernaola A.M., The GōMartini Approach: Revisiting the Concept of Contact Maps and the Modelling of Protein Complexes, ACTA PHYSICA POLONICA A, ISSN: 0587-4246, DOI: 10.12693/APhysPolA.145.S9, Vol.145, No.3, pp.S9-S20, 2024

Streszczenie:
We present a review of a series of contact maps for the determination of native interactions in proteins and nucleic acids based on a distance threshold. Such contact maps are mostly based on physical and chemical construction, and yet they are sensitive to some parameters (e.g., distances or atomic radii) and can neglect some key interactions. Furthermore, we also comment on a new class of contact maps that only requires geometric arguments. The contact map is a necessary ingredient to build a robust Gō-Martini model for proteins and their complexes in the Martini 3 force field. We present the extension of a popular structure-based Gō--like approach to the study of protein–sugar complexes, and the limitations of this approach are also discussed. The Gō-Martini approach was first introduced by Poma et al. (J. Chem. Theory Comput. 13, 1366 (2017)) in Martini 2 force field, and recently, it has gained the status of gold standard for protein simulation undergoing conformational changes in Martini 3 force field. We discuss several studies that have provided support for this approach in the context of the biophysical community.

Słowa kluczowe:
Martini 3,Structure-based coarse-graining,SMFS,biomolecules,GoMartini

Afiliacje autorów:
Cofas Vargas L.F. - inna afiliacja
Azevedo Rodrigo M. - inna afiliacja
Poblete S. - inna afiliacja
Chwastyk M. - Institute of Physics, Polish Academy of Sciences (PL)
Poma Bernaola A.M. - inna afiliacja
70p.
2.  Moreira R., Chwastyk M., Baker J.L., Vargas Guzman H.A., Poma A., Quantitative determination of mechanical stability in the novel coronavirus spike protein, NANOSCALE, ISSN: 2040-3364, DOI: 10.1039/D0NR03969A, Vol.12, No.31, pp.16409-16413, 2020

Streszczenie:
We report on the novel observation about the gain in mechanical stability of the SARS-CoV-2 (CoV2) spike (S) protein in comparison with SARS-CoV from 2002 (CoV1). Our findings have several biological implications in the subfamily of coronaviruses, as they suggest that the receptor binding domain (RBD) (~200 amino acids) plays a fundamental role as a damping element of the massive viral particle's motion prior to cell-recognition, while also facilitating viral attachment, fusion and entry. The mechanical stability via pulling of the RBD is 250 pN and 200 pN for CoV2 and CoV1 respectively, and the additional stability observed for CoV2 (~50 pN) might play a role in the increasing spread of COVID-19.

Afiliacje autorów:
Moreira R. - IPPT PAN
Chwastyk M. - Institute of Physics, Polish Academy of Sciences (PL)
Baker J.L. - The College of New Jersey (US)
Vargas Guzman H.A. - Max-Planck-Institute for Polymer Research (DE)
Poma A. - IPPT PAN
140p.
3.  Poma Bernaola A., Chwastyk M., Cieplak M., Elastic moduli of biological fibers in a coarse-grained model: crystalline cellulose and β-amyloids, Physical Chemistry Chemical Physics, ISSN: 1463-9076, DOI: 10.1039/C7CP05269C, Vol.19, pp.28195-28206, 2017

Streszczenie:
We study the mechanical response of cellulose and β-amyloid microfibrils to three types of deformation: tensile, indentational, and shear. The cellulose microfibrils correspond to the allomorphs Iα or Iβ whereas the β-amyloid microfibrils correspond to the polymorphs of either two- or three-fold symmetry. This response can be characterized by three elastic moduli, namely, YL, YT, and S. We use a structure-based coarse-grained model to analyze the deformations in a unified manner. We find that each of the moduli is almost the same for the two allomorphs of cellulose but YL is about 20 times larger than YT (140 GPa vs. 7 GPa), indicating the existence of significant anisotropy. For cellulose we note that the anisotropy results from the involvement of covalent bonds in stretching. For β-amyloid, the sense of anisotropy is opposite to that of cellulose. In the three-fold symmetry case, YL is about half of YT (3 vs. 7) whereas for two-fold symmetry the anisotropy is much larger (1.6 vs. 21 GPa). The S modulus is derived to be 1.2 GPa for three-fold symmetry and one half of it for the other symmetry and 3.0 GPa for cellulose. The values of the moduli reflect deformations in the hydrogen-bond network. Unlike in our theoretical approach, no experiment can measure all three elastic moduli with the same apparatus. However, our theoretical results are consistent with various measured values: typical YL for cellulose Iβ ranges from 133 to 155 GPa, YT from 2 to 25 GPa, and S from 1.8 to 3.8 GPa. For β-amyloid, the experimental values of S and YT are about 0.3 GPa and 3.3 GPa respectively, while the value of YL has not been reported.

Słowa kluczowe:
Tensile, shear, indentation, Atomic Force Microscopy, amyloid, cellulose

Afiliacje autorów:
Poma Bernaola A. - inna afiliacja
Chwastyk M. - Institute of Physics, Polish Academy of Sciences (PL)
Cieplak M. - Institute of Physics, Polish Academy of Sciences (PL)
40p.
4.  Poma Bernaola A., Chwastyk M., Cieplak M., Coarse-grained model of the native cellulose and the transformation pathways to the allomorph, CELLULOSE, ISSN: 0969-0239, DOI: 10.1007/s10570-016-0903-4, Vol.23, pp.1573-1591, 2016

Streszczenie:
All-atom simulations are used to derive effective parameters for a coarse-grained description of the crystalline cellulose I

Słowa kluczowe:
Cellulose, microfibril, allomorphs, structural transition, molecular dynamics, free energy

Afiliacje autorów:
Poma Bernaola A. - inna afiliacja
Chwastyk M. - Institute of Physics, Polish Academy of Sciences (PL)
Cieplak M. - Institute of Physics, Polish Academy of Sciences (PL)
45p.
5.  Poma Bernaola A., Chwastyk M., Cieplak M., Polysaccharide–protein complexes in a Coarse-Grained Model, JOURNAL OF PHYSICAL CHEMISTRY B, ISSN: 1520-6106, DOI: 10.1021/acs.jpcb.5b06141, Vol.119, pp.12028-12041, 2015

Streszczenie:
We construct two variants of coarse-grained models of three hexaoses: one based on the centers of mass of the monomers and the other associated with the C4 atoms. The latter is found to be better defined and more suitable for studying interactions with proteins described within α-C based models. We determine the corresponding effective stiffness constants through all-atom simulations and two statistical methods. One method is the Boltzmann inversion (BI) and the other, named energy-based (EB), involves direct monitoring of energies as a function of the variables that define the stiffness potentials. The two methods are generally consistent in their account of the stiffness. We find that the elastic constants differ between the hexaoses and are noticeably different from those determined for the crystalline cellulose Iβ. The nonbonded couplings through hydrogen bonds between different sugar molecules are modeled by the Lennard-Jones potentials and are found to be stronger than the hydrogen bonds in proteins. We observe that the EB method agrees with other theoretical and experimental determinations of the nonbonded parameters much better than BI. We then consider the hexaose-Man5B catalytic complexes and determine the contact energies between their the C4−α-C atoms. These interactions are found to be stronger than the proteinic hydrogen bonds: about four times as strong for cellohexaose and two times for mannohexaose. The fluctuational dynamics of the coarse-grained complexes are found to be compatible with previous all-atom studies by Bernardi et al.

Słowa kluczowe:
Polysaccharide, protein, principal component analysis, coarse graining, molecular simulation

Afiliacje autorów:
Poma Bernaola A. - inna afiliacja
Chwastyk M. - Institute of Physics, Polish Academy of Sciences (PL)
Cieplak M. - Institute of Physics, Polish Academy of Sciences (PL)
30p.
6.  Chwastyk M., Poma Bernaola A., Cieplak M., Statistical radii associated with amino acids to determine the contact map: fixing the structure of a type I cohesin domain in the Clostridium thermocellum cellulosome, PHYSICAL BIOLOGY, ISSN: 1478-3967, DOI: 10.1088/1478-3975/12/4/046002, Vol.12, No.046002, pp.1-11, 2015

Streszczenie:
We propose to improve and simplify protein refinement procedures through consideration of which pairs of amino acid residues should form native contacts. We first consider 11 330 proteins from the CATH database to determine statistical distributions of contacts associated with a given type of amino acid. The distributions are set across the distances between the α-C atoms that are in contact. Based on this data, we determine typical radii of effective spheres that can be placed on the α-C atoms in order to reconstruct the distribution of the contact lengths. This is done by checking for overlaps with enlarged van der Waals spheres associated with heavy atoms on other amino acids.The resulting contacts can be used to identify non-native contacts that may arise during the time evolution of structure-based models. Here, the radii are used to guide reconstruction of nine missing side chains in a type I cohesin domain with the Protein Data Bank code 1AOH. We first identify the likely missing contacts and then sculpt the corresponding side chains by standard refinement tools to achieve consistency with the expected contact map. One ambiguity in refinement is resolved by determining all-atom conformational energies.

Słowa kluczowe:
Cohesin, Go-like model, protein prediction, proteins, AFM, stretching

Afiliacje autorów:
Chwastyk M. - Institute of Physics, Polish Academy of Sciences (PL)
Poma Bernaola A. - inna afiliacja
Cieplak M. - Institute of Physics, Polish Academy of Sciences (PL)
25p.

Kategoria A Plus

IPPT PAN

logo ippt            ul. Pawińskiego 5B, 02-106 Warszawa
  +48 22 826 12 81 (centrala)
  +48 22 826 98 15
 

Znajdź nas

mapka
© Instytut Podstawowych Problemów Techniki Polskiej Akademii Nauk 2024