CeNT Seminar (Thursday, September 3rd, 2026, 11:00 AM): The power of distance geometry to explore protein conformation

31 08 2026

The Centre of New Technologies, University of Warsaw invites to a seminar by:

prof. Thérèse E Malliavin

Laboratoire de Physique et Chimie Théoriques, CNRS and Université de Lorraine, France

Title: The power of distance geometry to explore protein conformation
Date: September 3, 2026
TIme: 11:00 (Central European Time)
Host: prof. Joanna Sułkowska

The seminar will be held in the 00.142 auditorium, Banacha 2c

Abstract: In structural biology, protein structure calculation is classically performed by optimization, and the convergence of solutions is the determining criterion for the reliability of the structure. However, this criterion cannot be applied to intrinsically disordered proteins (IDPs), because they adopt highly variable conformations with similar energies. Solving the distance geometry problem (DGP) using the Threading-Augmented Interval Branch-and-Prune (TAiBP) approach allows for the systematic enumeration of possible IDP conformations from a set of NMR chemical shifts. The combinatorial explosion due to enumeration is mitigated by partitioning the input instances into consecutive peptide fragments and by systematically grouping the solutions using self-organizing maps. The resulting protein conformation sets can be further filtered using small-angle X-ray scattering (SAXS) curves or residual dipole coupling (RDC) values. Several applications will be presented.

The Branch-and-Prune (iBP) algorithm, on which TAiBP is based, has the unique feature of allowing the testing of the influence of any combination of bond and twist angles on protein conformations. The iBP algorithm thus makes it possible to calculate protein conformations using only knowledge of local conformations. In this case, the calculation efficiency is directly linked to knowledge of the stereochemistry (bond angles and dihedral angles ω) along the protein sequence and is particularly sensitive to variations in the dihedral angles ω. The impact of stereochemical variations is particularly pronounced in
the case of protein topologies defined by numerous long-range constraints,such as in the case of proteins with β secondary structures.

References:

Botnari, Sibille, Lin, Malliavin. Filtering disordered protein conformations by NMR residual dipolar couplings. accepted at J Phys Chem B.
Huang, Shih, Jeng, Chang, Lin, Malliavin. pH Sensitivity of the SERF1a Conformational Ensemble. ACS Omega 2026 11:2614-2627. doi: 10.1021/acsomega.5c07620
Förster, Idier, Liberti, Mucherino, Lin, Malliavin. Low-resolution description of the conformational space for intrinsically disordered proteins. Sci Rep 2022 12:19057. doi: 10.1038/s41598-022-21648-9
Malliavin. Tandem domain structure determination based on a systematic enumeration of conformations. Sci Rep 2021 11:16925. doi: 10.1038/s41598-021-96370-z
Malliavin, Mucherino, Lavor, Liberti. Systematic Exploration of Protein Conformational Space Using a Distance Geometry Approach. J Chem Inf Model 2019 59:4486-4503 doi: 10.1021/acs.jcim.9b00215