Cadherin-11 dimerization multi-site kinetics: combined partial unfolding and strand-swapping

Cadherin extracellular domain 1 (EC1) mediates dimerization of type II cadherins between opposing cell surfaces to facilitate cell-cell adhesion. EC1 forms domain-swapped dimers, with residues Trp2 and Trp4 crucial to anchor the EC1 A-strand in the strand-swapped conformation. In the present work, the specific roles of Trp2 and Trp4 in the dimerization mechanism of Cadherin-11 have been elucidated using NMR spectroscopy of wild-type and designed mutant EC1 domains. The results show that the dominant monomeric state, with the A strand and Trp side chains packed intramolecularly, is in equilibrium with a sparsely populated (1.6%) partially strand-exposed state, in which the Trp2 side chain packing is disrupted and with a sparsely populated (1.6%) fully strand-exposed state, in which the A strand, Trp2 and Trp4 side chain packing are fully disrupted. The exchange kinetics between the major state and the partially strand-exposed state are slow-intermediate (kex = 700 – 734 s-1) and the exchange kinetics between the major state and the fully strand-exposed state are intermediate-fast (kex = 3470 - 3591 s-1,) on the NMR chemical shift time scale. These three conformations, varying in the degree of A-strand exposure, also are coupled to additional conformational states on very fast and very slow timescales. The very fast exchange process arises from interconversion between ordered and random coil conformations of the BC loop in proximity to the Trp2 binding pocket, with relative populations that depend on the extent of A-strand exposure and dimerization status. The very slow exchange processes link the folded partially and fully strand-exposed conformations with partially unfolded conformational states, which have been recognized as crucial intermediates for domain-swapping in proteins other than cadherins. This framework reveals the dimerization mechanism of type II Cadherins as coupled folding and strand-swapping.

FASPR: an open-source tool for fast and accurate protein side-chain packing

Motivation Protein structure and function are essentially determined by how the side-chain atoms interact with each other. Thus, accurate protein side-chain packing (PSCP) is a critical step toward protein structure prediction and protein design. Despite the importance of the problem, however, the accuracy and speed of current PSCP programs are still not satisfactory. Results We present FASPR for fast and accurate PSCP by using an optimized scoring function in combination with a deterministic searching algorithm. The performance of FASPR was compared with four state-of-the-art PSCP methods (CISRR, RASP, SCATD and SCWRL4) on both native and non-native protein backbones. For the assessment on native backbones, FASPR achieved a good performance by correctly predicting 69.1% of all the side-chain dihedral angles using a stringent tolerance criterion of 20°, compared favorably with SCWRL4, CISRR, RASP and SCATD which successfully predicted 68.8%, 68.6%, 67.8% and 61.7%, respectively. Additionally, FASPR achieved the highest speed for packing the 379 test protein structures in only 34.3 s, which was significantly faster than the control methods. For the assessment on non-native backbones, FASPR showed an equivalent or better performance on I-TASSER predicted backbones and the backbones perturbed from experimental structures. Detailed analyses showed that the major advantage of FASPR lies in the optimal combination of the dead-end elimination and tree decomposition with a well optimized scoring function, which makes FASPR of practical use for both protein structure modeling and protein design studies. Availability and implementation The web server, source code and datasets are freely available at https://zhanglab.ccmb.med.umich.edu/FASPR and https://github.com/tommyhuangthu/FASPR. Supplementary information Supplementary data are available at Bioinformatics online.