CC+ : A searchable database of validated coiled coils in PDB structures and AlphaFold2 models

α-Helical coiled coils are common tertiary and quaternary elements of protein structure. In coiled coils, two or more α helices wrap around each other to form bundles. This apparently simple structural motif can generate many architectures and topologies. Coiled coil-forming sequences can be predicted from heptad repeats of hydrophobic and polar residues, hpphppp, although this is not always reliable. Alternatively, coiled-coil structures can be identified using the program SOCKET, which finds knobs-into-holes (KIH) packing between side chains of neighboring helices. SOCKET also classifies coiled-coil architecture and topology, thus allowing sequence-to-structure relationships to be garnered. In 2009, we used SOCKET to create a relational database of coiled-coil structures, CC+ , from the RCSB Protein Data Bank (PDB). Here, we report an update of CC+ following an update of SOCKET (to Socket2) and the recent explosion of structural data and the success of AlphaFold2 in predicting protein structures from genome sequences. With the most-stringent SOCKET parameters, CC+ contains ≈12,000 coiled-coil assemblies from experimentally determined structures, and ≈120,000 potential coiled-coil structures within single-chain models predicted by AlphaFold2 across 48 proteomes. CC+ allows these and other less-stringently defined coiled coils to be searched at various levels of structure, sequence, and side-chain interactions. The identified coiled coils can be viewed directly from CC+ using the Socket2 application, and their associated data can be downloaded for further analyses. CC+ is available freely at http://coiledcoils.chm.bris.ac.uk/CCPlus/Home.html. It will be updated automatically. We envisage that CC+ could be used to understand coiled-coil assemblies and their sequence-to-structure relationships, and to aid protein design and engineering.

Understanding a protein fold: the physics, chemistry, and biology of α-helical coiled coils

Protein science is being transformed by powerful computational methods for structure prediction and design: AlphaFold2 can predict many natural protein structures from sequence, and other AI methods are enabling the de novo design of new structures. This raises a question: how much do we understand the underlying sequence-to-structure/function relationships being captured by these methods? This perspective presents our current understanding of one class of protein assembly, the α-helical coiled coils. At first sight, these are straightforward: sequence repeats of hydrophobic (h) and polar (p) residues, (hpphppp)_n, direct the folding and assembly of amphipathic α helices into bundles. However, many different bundles are possible: they can have two or more helices (different oligomers); the helices can have parallel, antiparallel or mixed arrangements (different topologies); and the helical sequences can be the same (homomers) or different (heteromers). Thus, sequence-to-structure relationships must be present within the hpphppp repeats to distinguish these states. I discuss the current understanding of this problem at three levels: First, physics gives a parametric framework to generate the many possible coiled-coil backbone structures. Second, chemistry provides a means to explore and deliver sequence-to-structure relationships. Third, biology shows how coiled coils are adapted and functionalized in nature, inspiring applications of coiled coils in synthetic biology. I argue that the chemistry is largely understood; the physics is partly solved, though the considerable challenge of predicting even relative stabilities of different coiled-coil states remains; but there is much more to explore in the biology and synthetic biology of coiled coils.

Dynamic Regulation of Long-Chain Fatty Acid Oxidation by a Noncanonical Interaction between the MCL-1 BH3 Helix and VLCAD

MCL-1 is a BCL-2 family protein implicated in the development and chemoresistance of human cancer. Unlike its anti-apoptotic homologs, Mcl-1 deletion has profound physiologic consequences, indicative of a broader role in homeostasis. We report that the BCL-2 homology 3 (BH3) α helix of MCL-1 can directly engage very long-chain acyl-CoA dehydrogenase (VLCAD), a key enzyme of the mitochondrial fatty acid β-oxidation (FAO) pathway. Proteomic analysis confirmed that the mitochondrial matrix isoform of MCL-1 (MCL-1^Matrix) interacts with VLCAD. Mcl-1 deletion, or eliminating MCL-1^Matrix alone, selectively deregulated long-chain FAO, causing increased flux through the pathway in response to nutrient deprivation. Transient elevation in MCL-1 upon serum withdrawal, a striking increase in MCL-1 BH3/VLCAD interaction upon palmitic acid titration, and direct modulation of enzymatic activity by the MCL-1 BH3 α helix are consistent with dynamic regulation. Thus, the MCL-1 BH3 interaction with VLCAD revealed a separable, gain-of-function role for MCL-1 in the regulation of lipid metabolism.

Stabilized helical peptides: a strategy to target protein-protein interactions

Protein-protein interactions are critical for cell proliferation, differentiation, and function. Peptides hold great promise for clinical applications focused on targeting protein-protein interactions. Advantages of peptides include a large chemical space and potential diversity of sequences and structures. However, peptides do present well-known challenges for drug development. Progress has been made in the development of stabilizing alpha helices for potential therapeutic applications. Advantages and disadvantages of different methods of helical peptide stabilization are discussed.

Origin of the voltage dependence of G-protein regulation of P/Q-type Ca2+ channels

G-protein (Gbetagamma)-mediated voltage-dependent inhibition of N- and P/Q-type Ca(2+) channels contributes to presynaptic inhibition and short-term synaptic plasticity. The voltage dependence derives from the dissociation of Gbetagamma from the inhibited channels, but the underlying molecular and biophysical mechanisms remain largely unclear. In this study we investigated the role in this process of Ca(2+) channel beta subunit (Ca(v)beta) and a rigid alpha-helical structure between the alpha-interacting domain (AID), the primary Ca(v)beta docking site on the channel alpha(1) subunit, and the pore-lining IS6 segment. Gbetagamma inhibition of P/Q-type channels was reconstituted in giant inside-out membrane patches from Xenopus oocytes. Large populations of channels devoid of Ca(v)beta were produced by washing out a mutant Ca(v)beta with a reduced affinity for the AID. These beta-less channels were still inhibited by Gbetagamma, but without any voltage dependence, indicating that Ca(v)beta is indispensable for voltage-dependent Gbetagamma inhibition. A truncated Ca(v)beta containing only the AID-binding guanylate kinase (GK) domain could fully confer voltage dependence to Gbetagamma inhibition. Gbetagamma did not alter inactivation properties, and channels recovered from Gbetagamma inhibition exhibited the same activation property as un-inhibited channels, indicating that Gbetagamma does not dislodge Ca(v)beta from the inhibited channel. Furthermore, voltage-dependent Gbetagamma inhibition was abolished when the rigid alpha-helix between the AID and IS6 was disrupted by insertion of multiple glycines, which also eliminated Ca(v)beta regulation of channel gating, revealing a pivotal role of this rigid alpha-helix in both processes. These results suggest that depolarization-triggered movement of IS6, coupled to the subsequent conformational change of the Gbetagamma-binding pocket through a rigid alpha-helix induced partly by the Ca(v)beta GK domain, causes the dissociation of Gbetagamma and is fundamental to voltage-dependent Gbetagamma inhibition.

Computational estimation of specific side chain interaction energies in alpha helices

We have used a structure energy-based computer program developed for protein design, Perla, to provide theoretical estimates of all specific side chain-side chain interaction energies occurring in alpha helices. The computed side chain-side chain interaction energies were used as substitutes for the corresponding values used by the helix/coil transition algorithm, AGADIR. Predictions of peptide helical contents were nearly as successful as those obtained with the originally calibrated set of parameters; a correlation to experimentally observed alpha-helical populations of 0.91 proved that our theoretical estimates are reasonably correct for amino acid pairs that are frequent in our database of peptides. Furthermore, we have determined experimentally the previously uncharacterized interaction energies for Lys-Ile, Thr-Ile, and Phe-Ile amino acid pairs at i,i + 4 positions. The experimental values compare favorably with the computed theoretical estimates. Importantly, the computed values for Thr-Ile and Phe-Ile interactions are better than the energies based on chemical similarity, whereas for Lys-Ile they are similar. Thus, computational techniques can be used to provide precise energies for amino acid pairwise interactions, a fact that supports the development of structure energy-based computational tools for structure predictions and sequence design.

The Use of Structural Templates in Protein Backbone Modeling

The procedures used to model a protein structure are well established when the novel protein has high sequence similarity to a protein of known structure. Many proteins of interest have low (i.e. <50%) sequence similarity to any known structure. In these cases new approaches to prediction of structure are required. The use of sequence profiles which relate sequence to known structure has been proposed as one method to assign local regions of structure. As a first stage, templates or "icons" of the many relevant substructural motifs found in proteins must be defined. The sequences which gave rise to these structures are then aligned and a weighted profile obtained. Average structures of the 8 and 12 residue helix-turn and turn-helix motifs have been prepared. These coordinate templates were then used to scan through the Brookhaven protein structural database for similar, superimposable fragments. A composite template of 100 similar fragments for each element was found to be internally consistent to a rmsd=0.92 Å for HT8, 1.54 Å for HT12, 0.41 Å for TH8 and 1.40 Å for TH12. All of the sequences, from these structures, were then used to create an overall sequence profile. The four sequence profiles were scanned against the amino acid sequences of the proteins in the Brookhaven database: tertiary structure was correctly identified only about 10% of the time. This value is too low for predictive purposes. However, it could be increased by checking for multiple occurrences of the template in one protein.

Prediction of secondary structure of proteins. A comparison of the phi, psi angles previously predicted for cytochrome c with recent x-ray crystallographic findings

Newer data from the x-ray crystallographic studies of tuna heart ferrocytochrome c have increased the number of residues in alpha-helical segments. This provided an objective test of our method of predicting varphi,Psi values for cytochrome c using the sequences of 18 cytochromes c and twenty 20 x 20 tables for the varphi,Psi values of tripeptides in 10 other proteins whose three-dimensional structures were known from x-ray crystallographic studies. Of the 32 residues now considered from x-ray data to be in alpha-helices, 27 had been predicted to be in the alpha-helical domain.