Biology subjects

Kelch, B. A.

Publications and source records attributed to Kelch, B. A..

At least 19 recordsLinked to original sources

bioRxiv2025

SARM1, the executioner of axon degeneration, is an ADP-ribosyl transferase and autoMARylation negatively regulates its activation

Axon degeneration is a hallmark of nearly all neurodegenerative diseases. SARM1 plays a central role in this process by degrading NAD+ into nicotinamide and ADPR or cADPR. SARM1 also catalyzes a base exchange reaction between NAD+-phosphate (NADP+) and nicotinic acid (NA) to generate NAADP. These second messengers (i.e., ADPR, cADPR, and NAADP), and NAD+ consumption, are thought to drive axon degeneration. Herein, we identify a fourth reaction catalyzed by SARM1: mono-ADP-ribosylation (MARylation). Specifically, we show that SARM1 MARylates itself and other proteins with a catalytic efficiency (kcat/Km) higher than its NAD+ hydrolase activity. We further show that auto-MARylation promotes a phase transition and renders SARM1 responsive to regulation by NMN. Notably, endogenous SARM1 is MARylated at mitochondria, suggesting that MARylation may regulate SARM1 localization. Together, these findings uncover new regulatory mechanisms and expand the known signaling functions of SARM1. SignificanceSARM1 is an NAD+ hydrolase that executes axon degeneration in myriad neurodegenerative diseases. In addition to NAD+ hydrolysis, SARM1 catalyzes NAD+ cyclization and a base exchange reaction with NADP+ and nicotinic acid. These studies show that SARM1 also catalyzes the transfer of single ADPR moieties to proteins, including itself. Notably, we show that this auto-modification regulates SARM1 activity, allowing the protein to respond to NMN and to permit the phase transition. We also show that endogenous SARM1 is modified at the mitochondria, suggesting that this post-translational modification regulates SARM1 subcellular localization. These findings offer valuable mechanistic insights into SARM1 regulation that will ultimately inform the development of inhibitors targeting SARM1 for neurodegenerative diseases.

biochemistry↗

bioRxiv2025

Regulation of tension-dependent localization of LATS1 and LATS2 to adherens junctions.

The LIM domain protein LIMD1 is a critical regulator of the Hippo signaling pathway, acting to sequester the kinases LATS1/2 to adherens junctions (AJs) in response to mechanical strain. Here, we identify the molecular basis for LIMD1 binding and recruitment of LATS1/2 to AJs. We show that while the LIM domains of LIMD1 are sufficient for AJ localization and binding to LATS1/2, recruitment of LATS1 to AJ requires both the intrinsically disordered region (IDR) in the N-terminus as well as the LIM domains. We further dissected the LIM domains and found that LIM1 and LIM2, but not LIM3, are necessary for LATS1 AJ localization. Point mutations that disrupt strain sensitivity in either the first or second LIM domain disrupt both binding and recruitment of LATS1/2 to AJs. Mechanistically, LIMD1 binds LATS1/2 through a conserved linear motif, the LATS-LATCH, which we identified by AlphaFold modeling and confirmed by biochemical and localization assays. The LATS-LATCH is both necessary and sufficient for strain-dependent recruitment of LATS1/2 to AJs. Mutation of predicted contact residues within the LATS-LATCH both disrupts its binding to LIMD1 and localization to AJs. These findings define a bipartite mechanism for LIMD1-dependent recruitment of LATS1/2 involving LIM domain-LATCH interactions and N-terminal IDR functions, providing insight into how mechanical signals are transduced through the Hippo pathway.

cell biology↗

bioRxiv2025

Cooperativity and Communication between the Active Sites of the Dimeric SARS-CoV-2 Main Protease

The coronaviral main protease (Mpro) is essential for the replication of the virus, and has been the subject of various biochemical, structural and enzymatic studies, as well as a drug target against SARS-CoV-2 infections. SARS-CoV-2 Mpro is known to be active as a dimer, with the N terminus of one protomer completing a key active site pocket of the other protomer. Despite apparent cooperativity in catalytic activity, how the two distal active sites in the dimer communicate and might be modulating binding and/or catalysis at the other remain to be clarified. Here, we have investigated the interplay between cooperativity, dimerization, and substrate cleavage in SARS-CoV-2 Mpro through a combination of enzymatic assays, crystal structures, and protein characterization. To disentangle the contribution of each active site to the observed enzymatic activity, we developed a cleavage assay involving heterodimers of active and inactive (C145A or inhibitor-bound) monomers. Strikingly, we found that heterodimerization increased cleavage efficiency per active monomer. Additionally, we mapped a network of critical residues bridging the two active sites and probed this network through engineered mutations. By dissecting the cooperativity and communication between the active sites, we provide new insights into the Mpro reaction cycle and functional significance of its dimeric architecture.

biochemistry↗

bioRxiv2025

PCNA is a Nucleotide Exchange Factor for the Clamp Loader ATPase Complex

All life requires loading ring-shaped sliding clamp protein complexes onto DNA. The sliding clamp loader is a conserved AAA+ ATPase that binds the sliding clamp, opens the ring, and places it onto DNA. While recent structural work on both the canonical and alternative clamp loaders has shed light into how these machines perform their task once, it remains unclear how clamp loaders are recycled to load multiple sliding clamps. Here, we present structures of the Saccharomyces cerevisiae clamp loader Replication Factor C (RFC) in absence of sliding clamp or supplemented nucleotide. Our structures indicate that RFC holds onto ADP tightly in at least two of its four ATPase active sites, suggesting that nucleotide exchange is regulated. Our molecular dynamics simulations and biochemical data indicate that binding of the sliding clamp PCNA causes rapid exchange of tightly bound ADP. Our data suggests that PCNA acts as a nucleotide exchange factor by prying apart adjacent subunits, providing a pathway for ADP release. We propose that, by using its own substrate as a nucleotide exchange factor, RFC excludes off-pathway states that would arise from binding DNA prior to PCNA.

biochemistry↗

bioRxiv2025

The structure of a thermostable phage's Portal Vertex and Neck Complex illuminates its maturation process

Viruses assemble from component parts inside their host cells, but the mechanisms coordinating this complex process are not completely understood. In tailed bacteriophages, the genome is packaged into its capsid shell through the portal complex. The portal complex then closes to retain DNA and connects to the tail, which is required for host recognition and infection. The trigger to stop pumping DNA and assemble the mature virus has been a longstanding conundrum in the field. We determined the structure of the portal, the proteins that connect it to the tail, and portal vertex in the hyperthermophilic phage Oshimavirus using cryo-Electron Microscopy (cryo-EM). We find highly intertwined loop structures, like in a wicker basket, stabilizing the portal vertex against high temperatures. Moreover, we observe that the portal protrudes from the capsid in mature virions. We propose that portal is repositioned by packaged DNA, forming a pressure-sensitive switch that terminates genome packaging and triggers tail attachment in headful phages.

microbiology↗

bioRxiv2023

Dueling Endogenous Viral-Like Sequences Control Synaptic Plasticity

The function of a large part of most genomes, generally called "junk DNA", remains largely unknown. Much of this enigmatic DNA corresponds to transposons, which are considered genomic parasites. Here, we show the protein of the Ty1 retrotransposon Copia is enriched at the Drosophila neuromuscular junction and is transported across synapses. Unexpectedly, disrupting Copia expression results in increases in both synapse development and structural synaptic plasticity. Plasticity is kept in balance as Copia antagonizes the Drosophila Arc (activity-regulated cytoskeleton-associated protein) homolog, which is a transposon-derived gene. Our cryo-EM structure of the Copia capsid shows a shell with large cargo capacity and leads to a hypothesis for mutual antagonism of Arc and Copia capsid assembly. Our findings provide evidence that a fully functional transposon plays a role at synapses, suggesting that transposons and other types of junk DNA are essential to developmental and cellular processes.

neuroscience↗

bioRxiv2023

Differences in clamp loader mechanism between bacteria and eukaryotes

Clamp loaders are pentameric ATPases that place circular sliding clamps onto DNA, where they function in DNA replication and genome integrity. The central activity of a clamp loader is the opening of the ring-shaped sliding clamp, and the subsequent binding to primer-template (p/t)-junctions. The general architecture of clamp loaders is conserved across all life, suggesting that their mechanism is retained. Recent structural studies of the eukaryotic clamp loader Replication Factor C (RFC) revealed that it functions using a crab-claw mechanism, where clamp opening is coupled to a massive conformational change in the loader. Here we investigate the clamp loading mechanism of the E. coli clamp loader at high resolution using cryo-electron microscopy (cryo-EM). We find that the E. coli clamp loader opens the clamp using a crab-claw motion at a single pivot point, whereas the eukaryotic RFC loader uses motions distributed across the complex. Furthermore, we find clamp opening occurs in multiple steps, starting with a partly open state with a spiral conformation, and proceeding to a wide open clamp in a surprising planar geometry. Finally, our structures in the presence of p/t-junctions illustrate how clamp closes around p/t-junctions and how the clamp loader initiates release from the loaded clamp. Our results reveal mechanistic distinctions in a macromolecular machine that is conserved across all domains of life.

biochemistry↗

bioRxiv2022

Structure and assembly of an extremely long bacteriophage tail tube

Tail tube assembly is an essential step in the assembly of long-tailed bacteriophages. Limited structural and biophysical information has impeded an understanding of assembly and stability of their long, flexible tail tubes. The hyperthermophilic phage P74-26 is particularly intriguing as it has the longest tail of any known virus (nearly 1 m) and is the most stable known phage. Here, we present the structure of the P74-26 tail tube and introduce an in vitro system for studying the kinetics of tube assembly. Our high resolution cryo-EM structure provides insight into how the P74-26 phage achieves its flexibility and thermostability through assembly of flexible loops into neighboring rings through tight "ball-and-socket"-like interactions. Guided by this structure, and in combination with mutational, light scattering, and molecular dynamics simulations data, we propose a model for the assembly of conserved tube-like structures across phage and other entities possessing Tail Tube-like proteins. Our model proposes that formation of a full ring licenses the adoption of a tube elongation-competent conformation among the flexible loops and their corresponding sockets, which is further stabilized by an adjacent ring. Tail assembly is controlled by the cooperative interaction of dynamic intra- and inter-ring contacts. Given the structural conservation among tail tube proteins and tail-like structures, our model can explain the mechanism of high-fidelity assembly of long, stable tubes.

biophysics↗

bioRxiv2022

A second DNA binding site on RFC facilitates clamp loading at gapped or nicked DNA

Clamp loaders place circular sliding clamp proteins onto DNA so that clamp-binding partner proteins can synthesize, scan, and repair the genome. DNA with nicks or small single-stranded gaps are common clamp-loading targets in DNA repair, yet these substrates would be sterically blocked given the known mechanism for binding of primer-template DNA. Here, we report the discovery of a second DNA binding site in the yeast clamp loader Replication Factor C (RFC) that aids in binding to nicked or gapped DNA. This DNA binding site is on the external surface and is only accessible in the open conformation of RFC. Initial DNA binding at this site thus provides access to the primary DNA binding site in the central chamber. Furthermore, we identify that this site can partially unwind DNA to create an extended single-stranded gap for DNA binding in RFCs central chamber and subsequent ATPase activation. Finally, we show that deletion of the BRCT domain, a major component of the external DNA binding site, results in defective yeast growth in the presence of DNA damage where nicked or gapped DNA intermediates occur. We propose that RFCs external DNA binding site acts to enhance DNA binding and clamp loading, particularly at DNA architectures typically found in DNA repair.

biochemistry↗

bioRxiv2021

Cryo-EM structures reveal high-resolution mechanism of a DNA polymerase sliding clamp loader

Sliding clamps are ring-shaped protein complexes that are integral to the DNA replication machinery of all life. Sliding clamps are opened and installed onto DNA by clamp loader AAA+ ATPase complexes. However, how a clamp loader opens and closes the sliding clamp around DNA is still unknown. Here, we describe structures of the S. cerevisiae clamp loader Replication Factor C (RFC) bound to its cognate sliding clamp Proliferating Cell Nuclear Antigen (PCNA) en route to successful loading. RFC first binds to PCNA in a dynamic, closed conformation that blocks both ATPase activity and DNA binding. RFC then opens the PCNA ring through a large-scale crab-claw expansion of both RFC and PCNA that explains how RFC prefers initial binding of PCNA over DNA. Next, the open RFC:PCNA complex binds DNA and interrogates the primer-template junction using a surprising base-flipping mechanism. Our structures indicate that initial PCNA opening and subsequent closure around DNA do not require ATP hydrolysis, but are driven by binding energy. ATP hydrolysis, which is necessary for RFC release, is triggered by interactions with both PCNA and DNA, explaining RFCs switch-like ATPase activity. Our work reveals how a AAA+ machine undergoes dramatic conformational changes for achieving binding preference and substrate remodeling.

biochemistry↗

bioRxiv2020

Viral Packaging ATPases Utilize a Glutamate Switch to Couple ATPase Activity and DNA Translocation

Many viruses utilize ringed packaging ATPases to translocate double-stranded DNA into procapsids during replication. A critical step in the mechanochemical cycle of such ATPases is ATP binding, which causes a subunit within the motor to grip DNA tightly. Here, we probe the underlying molecular mechanism by which ATP binding is coupled to DNA gripping and show that a glutamate switch residue found in AAA+ enzymes is central to this coupling in viral packaging ATPases. Using free energy landscapes computed through molecular dynamics simulations, we determined the stable conformational state of the ATPase active site in apo, ATP-bound, and ADP-bound states. Our results show that the catalytic glutamate residue transitions from an inactive to an active pose upon ATP binding, and that a residue assigned as the glutamate switch is necessary for regulating the transition. Further, we identified via mutual information analyses the intramolecular signaling pathway mediated by the glutamate switch that is responsible for coupling ATP binding to conformational transitions of DNA-gripping motifs. We corroborated these predictions with both structural and functional experimental data. Specifically, we showed that the crystal structure of the ADP-bound P74-26 packaging ATPase is consistent with the predicted structural coupling from simulations, and we further showed that disrupting the predicted signaling pathway indeed decouples ATPase activity from DNA translocation activity in the {varphi}29 DNA packaging motor. Our work thus establishes a signaling pathway in viral DNA packaging motors that ensures coordination between chemical and mechanical events involved in viral DNA packaging.

biophysics↗

bioRxiv2020

CaMKII binds both substrates and effectors at the active site

Ca2+/calmodulin dependent protein kinase II (CaMKII) is a signaling protein required for long-term memory. Once activated by Ca2+/CaM, it sustains activity even after the Ca2+ dissipates. In addition to well-known autophosphorylation-mediated mechanism, interaction with specific binding partners also persistently activates CaMKII. A longstanding model invokes two distinct S- and T-sites. If an interactor binds at the T-site, it will preclude autoinhibition and allow substrates to be phosphorylated at the S-site. Here, we specifically test this model with X-ray crystallography, molecular dynamics simulations, and biochemistry. Our data are inconsistent with this model. Co-crystal structures of four different activators or substrates show that they all bind to a single continuous site across the kinase domain. We propose a mechanistic model that persistent CaMKII activity is facilitated by high affinity binding partners, which kinetically compete with autoinhibition by the regulatory segment to allow substrate phosphorylation.

biochemistry↗

bioRxiv2020

Exploring the evolutionary history of kinetic stability in the alpha-lytic protease family

In addition to encoding the final tertiary fold and stability, the primary sequence of a protein encodes the folding trajectory and kinetic barriers that determines the speed of folding. How these kinetic barriers are encoded by the sequence is not well understood. Here, we use evolutionary sequence variation in the alpha-lytic protease (LP) protein family to probe the relationship between sequence and energy landscape. LP has an unusual energy landscape: the native state of LP is not the most thermodynamically favored conformation and, instead, it remains folded due to a large kinetic barrier preventing unfolding. In order to fold, LP utilizes an N-terminal pro region of similar size to the protease itself that functions as a folding catalyst. Once folded, the pro region is removed, and the native state does not unfold on a biologically relevant timescale. Without the pro region, LP folds on the order of millennia. A phylogenetic search uncovers LP homologs with a wide range of pro-region sizes, including some with no pro region at all. In the resulting phylogenetic tree, these homologs cluster by pro-region size. Homologs naturally lacking pro regions are thermodynamically stable, fold much faster than LP, yet retain the same fold as LP. Key amino acids thought to contribute to LPs extreme kinetic stability are lost in these homologs, further supporting their role in kinetic stability. This study highlights how the entire energy landscape plays an important role in determining the evolutionary pressures on and changes to the protein sequence.

biophysics↗

bioRxiv2020

Atomistic Mechanism of Force Generation, Translocation, and Coordination in a Viral Genome Packaging Motor

Double-stranded DNA viruses package their genomes into pre-assembled capsids using virally-encoded ASCE ATPase ring motors. We present the first atomic-resolution crystal structure of a multimeric ring form of a viral dsDNA packaging motor and characterize its atomic-level dynamics via long timescale molecular dynamics simulations. Based on the results, we deduce an overall packaging mechanism that is driven by helical-to-planar transitions of the ring motor. These transitions are coordinated by inter-subunit interactions that regulate catalytic and force-generating events. Stepwise ATP binding to individual subunits increase their affinity for the helical DNA phosphate backbone, resulting in distortion away from the planar ring towards a helical configuration, inducing mechanical strain. Subsequent sequential hydrolysis events alleviate the accumulated mechanical strain, allowing a stepwise return of the motor to the planar conformation, translocating DNA in the process. This type of helical-to-planar mechanism could serve as a general framework for ring ATPases that exhibit burst-dwell dynamics.

molecular biology↗

bioRxiv2020

Structure of the human clamp loader bound to the sliding clamp: a further twist on AAA+ mechanism

DNA replication requires the sliding clamp, a ring-shaped protein complex that encircles DNA, where it acts as an essential cofactor for DNA polymerases and other proteins. The sliding clamp needs to be actively opened and installed onto DNA by a clamp loader ATPase of the AAA+ family. The human clamp loader Replication Factor C (RFC) and sliding clamp PCNA are both essential and play critical roles in several diseases. Despite decades of study, no structure of human RFC has been resolved. Here, we report the structure of human RFC bound to PCNA by cryo-EM to an overall resolution of ~3.4 [A]. The active sites of RFC are fully bound to ATP analogs, which is expected to induce opening of the sliding clamp. However, we observe the complex in a conformation prior to PCNA opening, with the clamp loader ATPase modules forming an over-twisted spiral that is incapable of binding DNA or hydrolyzing ATP. The autoinhibited conformation observed here has many similarities to a previous yeast RFC:PCNA crystal structure, suggesting that eukaryotic clamp loaders adopt a similar autoinhibited state early on in clamp loading. Our results point to a Limited Change/Induced Fit mechanism in which the clamp first opens, followed by DNA binding inducing opening of the loader to release auto-inhibition. The proposed change from an over-twisted to an active conformation reveals a novel regulatory mechanism for AAA+ ATPases. Finally, our structural analysis of disease mutations leads to a mechanistic explanation for the role of RFC in human health.

biochemistry↗

bioRxiv2019

A thermophilic phage uses a small terminase protein with a fixed helix-turn-helix geometry

Tailed bacteriophage use a DNA packaging motor to encapsulate their genome during viral particle assembly. The small terminase (TerS) component acts as a molecular matchmaker by recognizing the viral genome as well as the main motor component, the large terminase (TerL). How TerS binds DNA and the TerL protein remains unclear. Here, we identify the TerS protein of the thermophilic bacteriophage P74-26. TerSP76-26 oligomerizes into a nonamer that binds DNA, stimulates TerL ATPase activity, and inhibits TerL nuclease activity. Our cryo-EM structure shows that TerSP76-26 forms a ring with a wide central pore and radially arrayed helix-turn-helix (HTH) domains. These HTH domains, which are thought to bind DNA by wrapping the helix around the ring, are rigidly held in an orientation distinct from that seen in other TerS proteins. This rigid arrangement of the putative DNA binding domain imposes strong constraints on how TerSP76-26 can bind DNA. Finally, the TerSP76-26 structure lacks the conserved C-terminal {beta}-barrel domain used by other TerS proteins for binding TerL, suggesting that a well-ordered C-terminal {beta}-barrel domain is not necessary for TerS to carry out its function as a matchmaker.

biochemistry↗

bioRxiv2018

Principles for enhancing virus capsid capacity and stability from a thermophilic virus capsid structure

The capsids of double-stranded DNA viruses protect the viral genome from the harsh extracellular environment, while maintaining stability against the high internal pressure of packaged DNA. To elucidate how capsids maintain stability in an extreme environment, we used cryoelectron microscopy to determine the capsid structure of the thermostable phage P74-26 to 2.8-[A] resolution. We find the P74-26 capsid exhibits an overall architecture that is very similar to those of other tailed bacteriophages, allowing us to directly compare structures to derive the structural basis for enhanced stability. Our structure reveals lasso-like interactions that appear to function like catch bonds. This architecture allows the capsid to expand during genome packaging, yet maintain structural stability. The P74-26 capsid has T=7 geometry despite being twice as large as mesophilic homologs. Capsid capacity is increased through a novel mechanism with a larger, flatter major capsid protein. Our results suggest that decreased icosahedral complexity (i.e. lower T number) leads to a more stable capsid assembly.

biochemistry↗

bioRxiv2017

A hyperthermophilic phage decoration protein suggests common evolutionary origin with Herpesvirus Triplex proteins and an anti-CRISPR protein

Virus capsid proteins reproducibly self-assemble into regularly-shaped, stable shells that protect the viral genome from external environmental assaults, while maintaining the high internal pressure of the tightly packaged viral genome. To elucidate how capsids maintain stability under harsh conditions, we investigated the capsid components of a hyperthermophilic virus, phage P74-26. We determined the structure of a capsid protein gp87 and show that it has the same fold as trimeric decoration proteins that enhance the structural stability of capsids in many other phage, despite lacking significant sequence homology. We also find that gp87 is significantly more stable than its mesophilic homologs, reflecting the high temperature environment in which phage P74-26 thrives. Our analysis of the gp87 structure reveals that the core domain of the decoration protein is conserved in trimeric capsid components across numerous dsDNA viruses, including human pathogens such as Herpesviruses. Moreover, this core {beta}-barrel domain is found in the anti-CRISPR protein AcrIIC1, which suggests a mechanism for the evolution of this broad spectrum Cas9 inhibitor. Our work illustrates the principles for increased stability of a thermophilic decoration protein, and extends the evolutionary reach of the core trimeric decoration protein fold.

biochemistry↗