Applications of sequence coevolution in membrane protein biochemistry

Nicoludis, John M.; Gaudet, Rachelle

doi:10.1016/j.bbamem.2017.10.004

Cited by 33 publications

(25 citation statements)

References 173 publications

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“…The algorithm reproduces self pairings for 74% of all sequences in the alignment, averaged across 5 replicates, after iteration to convergence. This is on par with accuracy of partner detection for other proteins pairs performed by related algorithms (23,34) and supports the use of our model built from natural sequences. When the EC1/EC4 and EC2/EC3 interactions were paired in isolation, we found that the accuracy of matching was less than when the whole interface was used, indicating that both interfaces act in combination to achieve full specificity of the interface.…”

Section: Model Parameters Reveal Biochemical Interactions Underlying supporting

confidence: 78%

“…Furthermore, simulations can improve consistency when defining interface residues in a protein family. Computational methods based on residue coevolution have been useful in understanding the structure of Pcdhs, predicting the EC1/EC4 interaction and that the trans dimer architecture exists in nonclustered Pcdhs, both findings later confirmed experimentally (15,16,18,34). Coevolving residue pairs identify interprotein contacts (22,23) but can correspond to positions only in contact in certain conformations (35)(36)(37).…”

Section: Structures and MD Show That Pcdh Trans Interfaces Sample Amentioning

confidence: 88%

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Interaction specificity of clustered protocadherins inferred from sequence covariation and structural analysis

Nicoludis

Green

Walujkar

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

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Clustered protocadherins, a large family of paralogous proteins that play important roles in neuronal development, provide an important case study of interaction specificity in a large eukaryotic protein family. A mammalian genome has more than 50 clustered protocadherin isoforms, which have remarkable homophilic specificity for interactions between cellular surfaces. A large antiparallel dimer interface formed by the first 4 extracellular cadherin (EC) domains controls this interaction. To understand how specificity is achieved between the numerous paralogs, we used a combination of structural and computational approaches. Molecular dynamics simulations revealed that individual EC interactions are weak and undergo binding and unbinding events, but together they form a stable complex through polyvalency. Strongly evolutionarily coupled residue pairs interacted more frequently in our simulations, suggesting that sequence coevolution can inform the frequency of interaction and biochemical nature of a residue interaction. With these simulations and sequence coevolution, we generated a statistical model of interaction energy for the clustered protocadherin family that measures the contributions of all amino acid pairs at the interface. Our interaction energy model assesses specificity for all possible pairs of isoforms, recapitulating known pairings and predicting the effects of experimental changes in isoform specificity that are consistent with literature results. Our results show that sequence coevolution can be used to understand specificity determinants in a protein family and prioritize interface amino acid substitutions to reprogram specific protein–protein interactions.

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Section: Model Parameters Reveal Biochemical Interactions Underlying supporting

confidence: 78%

Section: Structures and MD Show That Pcdh Trans Interfaces Sample Amentioning

confidence: 88%

Interaction specificity of clustered protocadherins inferred from sequence covariation and structural analysis

Nicoludis

Green

Walujkar

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

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“…Computational methods based on residue coevolution predicted the EC1/EC4 interaction and established that the trans dimer architecture would be found in non-clustered Pcdhs, both findings later confirmed experimentally (14,15,18,29). Sequence coevolution methods for protein-protein interface determination are typically benchmarked by comparing highly coevolving residue pairs that are not due to intramolecular structural features to their inter-residue distances in experimentally-determined structures (30,31).…”

Section: Highly Coevolving Residue Pairs Are Frequently In Contact Inmentioning

confidence: 84%

Interaction specificity of clustered protocadherins inferred from sequence covariation and structural analysis

Nicoludis

Green

Walujkar

et al. 2018

Preprint

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Clustered protocadherins are a large family of paralogous proteins that play important roles in neuronal development. The more than 50 clustered protocadherin isoforms have remarkable homophilic specificity for interactions between cellular surfaces that is controlled by a large antiparallel dimer interface formed by the first four extracellular cadherin (EC) domains. To understand how specificity is achieved between the numerous paralogs, we used a combination of structural and computational approaches. Molecular dynamics simulations revealed that individual EC interactions are weak and go through binding and unbinding events, but together they form a stable complex through polyvalency. Using sequence coevolution, we generated a statistical model of interaction energy for the clustered protocadherin family that measures the contributions of all amino acid pairs in the interface. Our interaction energy model assesses specificity for all possible pairs of isoforms, recapitulating known pairings and predicting the effects of experimental changes in isoform specificity that are consistent with literature results. Our results show that sequence coevolution can be used to understand specificity determinants in a protein family and prioritize interface amino acid substitutions to reprogram specific protein-protein interactions. Clustered protocadherins (Pcdhs) are a large protein family (53 isoforms in humans) that play roles in vertebrate nervous system development, including neuronal survival, axon targeting, neuronal arborization, and dendritic self-avoidance (1-9). Dendritic self-avoidance is mediated by formation of a clustered Pcdh assembly between two dendrites (10). This assembly relies on individual recognition units formed in trans across two cellular membranes that consist of homodimers of the first four extracellular cadherin-repeat (EC) domains in an antiparallel arrangement ( Figure 1A). These homodimers are highly specific such that no cross interactions are observed in even the most similar isoforms (11-13). The trans EC1-4 interaction is also found in other non-clustered Pcdhs (14-16), which have roles in nervous system development and maintenance (17), indicating the importance of this recognition unit in cognitive function. Given that there are many isoforms per vertebrate genome, we sought to understand how specificity is achieved in this large interface.Structures of these recognition units (14,(18)(19)(20) have revealed idiosyncratic characteristics of individual dimer structures, such as the lack of the EC1/EC4 interaction in the structure of PcdhγA1 and PcdhγA8 (20) and the small interface of the EC2/EC3 interaction in PcdhγB3 (14). More subtle structural differences can be observed broadly between the three clustered Pcdh subfamilies, α, β, and γ (14,19,20). Based on the variety of interfaces found in the existing crystal structures (14,(18)(19)(20), it is possible that every isoform achieves specificity by adopting a different static interface conformation, or that isoforms sample a distributi...

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“…The scale of our sequence alignments allowed us to take a closer look at the functional relevance of the PSM in ABC exporters through sequence coevolution analysis. Many predictive techniques for classifying the structural and functional properties of specific sites through multisequence analysis have emerged in recent years [34]. The Evolutionary Trace method is one such approach that is particularly powerful because it can infer likely functionally important features from phylogenetic relations and information content through evolution of a family [35].…”

Section: Evolutionary Contact Predictions Show the Psm Connects Nbds mentioning

confidence: 99%

The peptide sensor motif stabilizes the outward-facing conformation of TmrAB

Millan

Francis

Thompson

et al. 2020

Preprint

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ATP binding cassette (ABC) transporters participate in many processes central to life including cell wall biosynthesis, lipid homeostasis, and drug efflux. Large conformational rearrangements accompany transport and allosterically couple substrate transport in the transmembrane region to dimerization of nucleotide binding domains (NBDs) nearly ~30-40Å away in the cytoplasm. How the two binding sites coordinate remains elusive, particularly in a class of ABC transporters with only one catalytically competent NBD, the asymmetric ABC transporters. The peptide transporter TmrAB from Thermus thermophilus is one such asymmetric transporter, and here we present biochemical evidence that substrate binding couples to ATP binding in nonequivalent ways through each half of the TmrAB heterodimer. Specifically, we show that this unique mechanism depends on a highly conserved electrostatic motif in a region previously termed the peptide sensor. In this conformationally dynamic region, we demonstrate that mutation of an absolutely conserved glycine in the catalytically active TmrA chain (G131A) accelerates ATPase activity while uncoupling substrate binding from ATP hydrolysis. Surprisingly, mutation of the conserved glycine in the non-functional TmrB chain (G116A) resulted in the opposite effect in which ATPase activity is decreased with little effect on substrate binding. Our findings highlight an intrinsic asymmetry extending beyond that of the NBDs in asymmetric ABC transporters and support a mechanism where the peptide sensor in each half of TmrAB plays different roles in substrate transport.

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Applications of sequence coevolution in membrane protein biochemistry

Cited by 33 publications

References 173 publications

Interaction specificity of clustered protocadherins inferred from sequence covariation and structural analysis

Interaction specificity of clustered protocadherins inferred from sequence covariation and structural analysis

Interaction specificity of clustered protocadherins inferred from sequence covariation and structural analysis

The peptide sensor motif stabilizes the outward-facing conformation of TmrAB

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