Faculty Collaboration Database

Conformational free-energy landscapes of a Na⁺/Ca²⁺ exchanger explain its alternating-access mechanism and functional specificity. Proc Natl Acad Sci U S A 2024 Apr 16;121(16):e2318009121

Date

04/08/2024

Pubmed ID

38588414

Pubmed Central ID

PMC11032461

DOI

10.1073/pnas.2318009121

Scopus ID

2-s2.0-85190324798 (requires institutional sign-in at Scopus site)   9 Citations

Abstract

Secondary-active transporters catalyze the movement of myriad substances across all cellular membranes, typically against opposing concentration gradients, and without consuming any ATP. To do so, these proteins employ an intriguing structural mechanism evolved to be activated only upon recognition or release of the transported species. We examine this self-regulated mechanism using a homolog of the cardiac Na⁺/Ca²⁺ exchanger as a model system. Using advanced computer simulations, we map out the complete functional cycle of this transporter, including unknown conformations that we validate against existing experimental data. Calculated free-energy landscapes reveal why this transporter functions as an antiporter rather than a symporter, why it specifically exchanges Na⁺ and Ca²⁺, and why the stoichiometry of this exchange is exactly 3:1. We also rationalize why the protein does not exchange H⁺ for either Ca²⁺ or Na⁺, despite being able to bind H⁺ and its high similarity with H⁺/Ca²⁺ exchangers. Interestingly, the nature of this transporter is not explained by its primary structural states, known as inward- and outward-open conformations; instead, the defining factor is the feasibility of conformational intermediates between those states, wherein access pathways leading to the substrate binding sites become simultaneously occluded from both sides of the membrane. This analysis offers a physically coherent, broadly transferable route to understand the emergence of function from structure among secondary-active membrane transporters.

Author List

Marinelli F, Faraldo-Gómez JD

Author

Fabrizio Marinelli PhD Associate Professor in the Biophysics department at Medical College of Wisconsin

MESH terms used to index this publication - Major topics in bold

Antiporters
Biological Transport
Membrane Transport Proteins
Protein Conformation
Sodium-Calcium Exchanger