Claudia Alleva's research while affiliated with Stockholm University and other places

... The simulations provided clues to the intriguing question of why a protein structurally similar to CLC-ec1, such as CLC F , transports fluoride instead of being inhibited by it. More recently, MiMiC-based QM/MM MD simulations have been extended to DgoT, a bacterial homolog of human SLC17 organic anion transporters 114,115 . Here, the simulations shed light on a key proton transfer process occurring in DgoT's transport cycle in which bond breaking and formation occur. ...

... Learning the CV while having no observation of the motion is difficult, and our previous efforts have been mostly centered on a supervised learning approach. 15,16 There are however some general principles for designing a good CV: i) a good CV should describe the conformational change such that all relevant states are separable and uniquely correspond to different points along the CV. 17 ii) a good CV for AWH or other adaptive biasing methods should contain the degrees of freedom that are responsible for the highest energetic or kinetic barriers. 13 An essential hurdle to overcome is that the space of degrees of freedom is very large (3N) and searching all possible configurations would be intangible for very large systems, such as proteins or other biomolecules. ...

... Noteworthy of these highly fluctuating regions is that the residues involved in the largest extent of conformational change do not reside within the central binding pocket. These residues instead predominantly line the AtSWEET13 periphery, echoing the importance of distant residues for evolved function in other proteins, including membrane transporters [32][33][34][35] . From the perspective of transporter structure, these residues occupy regions directly associated with gating dynamics and potential gating contacts. ...

... Although it has become clear that the entire energetic landscape of a transporter contributes to its substrate discrimination (39)(40)(41), most mutational studies focus on the binding site as the main source of specificity (20,37,38). Indeed, here we found that groups of mutations peripheral to the binding site act together to encode transport polyspecificity in the SMRs. ...

... The simulations provided clues to the intriguing question of why a protein structurally similar to CLC-ec1, such as CLC F , transports fluoride instead of being inhibited by it. More recently, MiMiC-based QM/MM MD simulations have been extended to DgoT, a bacterial homolog of human SLC17 organic anion transporters 114,115 . Here, the simulations shed light on a key proton transfer process occurring in DgoT's transport cycle in which bond breaking and formation occur. ...

... On the basis of the recent K + /H + exchanger structure in complex with K + (ref. 38) and MD simulations of Na + /H + exchangers 17,18,23,33 , Na + is thought to be coordinated entirely in the core domain between the cross-over helices and Asn237 and Asp238 residues. Overall, the structure of the transporter module and ion-binding site is entirely consistent with that of a typical mammalian NHE, with most structural differences located at the oligomerization interface ( Fig. 2e and Extended Data Fig. 5a). ...

... Upon closer inspection, we find that the TM7b tyrosine is a phenylalanine residue in around 30% of more distantly related GLUT5 homologs (Figure 4-figure supplement 2). Indeed, independent co-evolution analysis corroborates that Y296 and H386 residues are forming an interaction in the occluded state of GLUT5 (Mitrovic et al., 2022). Moreover, in yeast-based forward-evolution screens of hexose transporters, the equivalent residue to Y296 in TM7b was the only single-residue-variant uncovered with a shifted substrate preference from D-glucose toward D-xylose (Wang et al., 2016b;Wang et al., 2016a). ...

... Notably, the relaxed GLUT5 occluded state does not fall on the largest energetic barrier corresponding to the transition state ( Figure 5). However, in the presence of a substrate sugar, GLUT5 passes through a transition state that closely matches the occluded state of PfHT1 (McComas et al., 2022). Our analysis indicates that coevolution-driven MD simulations are detecting an energetic minimum for an occluded state prior to the transition state which has not yet been experimentally observed ( Figure 5-figure supplement 3). ...

... Averages were calculated over trajectories and replicas. Electrostatics of the WNK4-binding pocket was calculated using g_elpot [39]. Time course of the electrostatic potential in the binding pocket was evaluated by defining a spherical volume with a radius of 8 Å, centered at the geometric center of the residues comprising the binding pocket. ...

... Based on the findings from the study on the EEAT and SERT transporters [42,43] it is plausible to hypothesize a similar sequence of events involving sodium's role in solute recognition and transport for OCTN1. Initially, the Na+ binding pocket opens, allowing for the influx of water molecules. ...