Slipknot or Crystallographic Error: A Computational Analysis of the Plasmodium falciparum DHFR Structural Folds

• Published in: International journal of molecular sciences Vol. 23; no. 3; p. 1514
• Main Authors: Tata, Rolland B, Alsulami, Ali F, Sheik Amamuddy, Olivier, Blundell, Tom L, Tastan Bishop, Özlem
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 28.01.2022; MDPI
• Subjects: atypical folds; Bias; Computer applications; crystallographic error; Crystallography; Crystallography, X-Ray; Databases, Protein; Dihydrofolate reductase; Enzymes; Epistemology; Error analysis; Homology; Knots; Malaria; Models, Molecular; Molecular dynamics; Molecular Dynamics Simulation; NMR; Nuclear magnetic resonance; P. falciparum DHFR; PDB; Plasmodium falciparum - enzymology; Plasmodium falciparum - genetics; Protein Conformation; Protein Domains; Protein Folding; Proteins; Protozoan Proteins - chemistry; Protozoan Proteins - genetics; R&D; Reductases; Research & development; Residues; Sequence Alignment - methods; Sequence Analysis, Protein; Sequence Homology, Amino Acid; slipknots; Tetrahydrofolate Dehydrogenase - chemistry; Tetrahydrofolate Dehydrogenase - genetics; Topology; Tuberculosis; crystallographic error; atypical folds; P. falciparum DHFR; slipknots; PDB
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms23031514

The presence of protein structures with atypical folds in the Protein Data Bank (PDB) is rare and may result from naturally occurring knots or crystallographic errors. Proper characterisation of such folds is imperative to understanding the basis of naturally existing knots and correcting crystallographic errors. If left uncorrected, such errors can frustrate downstream experiments that depend on the structures containing them. An atypical fold has been identified in dihydrofolate reductase ( DHFR) between residues 20-51 (loop 1) and residues 191-205 (loop 2). This enzyme is key to drug discovery efforts in the parasite, necessitating a thorough characterisation of these folds. Using multiple sequence alignments (MSA), a unique insert was identified in loop 1 that exacerbates the appearance of the atypical fold-giving it a slipknot-like topology. However, DHFR has not been deposited in the knotted proteins database, and processing its structure failed to identify any knots within its folds. The application of protein homology modelling and molecular dynamics simulations on the DHFR domain of and those of two other organisms ( and ) that were used as molecular replacement templates in solving the DHFR structure revealed plausible unentangled or open conformations of these loops. These results will serve as guides for crystallographic experiments to provide further insights into the atypical folds identified.