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Almo, S. C.

Publications and source records attributed to Almo, S. C..

13 recordsLinked to original sources

Ligand binding remodels the oligomeric state and active site of Klebsiella pneumoniae azoreductase

Azo dyes are widespread in the environment, and humans ingest a range of these dyes present in food and drugs. The human gut microbiome significantly impacts the fate of ingested azo dyes primarily through the reduction of the azo bond (R-N=N-R'). Flavin-dependent azoreductases have been considered the key enzymatic drivers of this process. To challenge this paradigm, we constructed a sequence similarity network of known azoreductases and focused on AzoA of Klebsiella pneumoniae, a central representative within the gut microbiome cluster. Unexpectedly, K. pneumoniae AzoA displayed relatively low in vitro activity against a range of azo compounds. While the physiological implications remain unclear, these findings are consistent with the possibility that non-enzymatic mechanisms contribute substantially to azo compound reduction in the gut. Furthermore, structural characterization of AzoA, as a holoenzyme and in its substrate-bound state, revealed a previously unrecognized ligand-coupled mechanism involving remodeling of the active site and oligomeric state.

biochemistry↗

Expression of the human immunomodulatory protein, human B7-1 (CD80), accelerates neuroinflammation, synaptic loss, microvascular instability and lethality in a murine model of Alzheimers Disease

Immune-mediated inflammatory processes play a pivotal role in the pathogenesis of Alzheimers disease (AD). However, immune loci exhibit significant sequence diversity, with human proteins sharing only [~]45-70% identity with their murine orthologs. This divergence contributes to the inability of many established mouse models to accurately capture key neuroinflammatory mechanisms relevant to human AD. We recently identified that the human, but not murine, immunomodulatory protein B7-1 (CD80) activates the p75 neurotrophin receptor (p75), a function arising from evolutionary divergence in human B7-1. This discovery provides an opportunity to directly interrogate the role of this interaction in disease progression using a well-characterized murine model of mutant A{beta} overexpression (CRND8). We generated a mouse line in which murine B7-1 was replaced with a chimeric human:murine B7-1 that retains normal interactions with CTLA-4 and CD28, while gaining the ability to bind p75, and evaluated its effects in CRND8 mice. Expression of human:murine B7-1 in vivo resulted in increased lethality, accelerated neuroinflammation of resident glia, more rapid synaptic and dendritic loss, and enhanced microvascular compromise in the subiculum compared to CRND8 mice expressing murine B7-1. Together, these findings identify the human B7-1:p75 interaction as a previously unrecognized contributor to AD pathogenesis and a potential therapeutic target in a brain region critical for learning and memory that is affected in early stages of disease.

neuroscience↗

Glypican-1 upregulation elicited in response to a cell-impermeable kinase inhibitor and its overexpression enhance HIV-1 infection

Studies of herpes simplex virus (HSV) entry uncovered a previously unappreciated "outside-in" signaling pathway whereby activation of the calcium (Ca2+) responsive enzyme phospholipid scramblase 1 (PLSCR1), which is known to trigger the bidirectional movement of phosphatidylserines (PS) between the inner and outer leaflet of the plasma membrane, also induces the translocation and subsequent extracellular activation of intracellular proteins, including Akt. We hypothesized that HIV-1, which has been shown to elicit scramblase TMEM16F-mediated PS externalization, may trigger a similar "outside-in" signaling cascade involving exofacial kinase activity to promote its entry into CD4+ T cells. To study this process, we utilized a cell impermeable staurosporine analogue, alkyl-CIMSS, which is a broadly active kinase inhibitor that blocks HSV-induced exofacial Akt phosphorylation and HSV infection. Using multiple cell types including TZM-bl, Jurkat T cells, and human peripheral blood mononuclear cells (PBMCs), we show that, in contrast to the effects on HSV, treatment of cells with alkyl-CIMSS enhances HIV-1 infection post-entry that is not dependent on TMEM16F. To identify potential biological processes that are responsive to alkyl-CIMSS, we performed bulk RNA-sequencing and whole cell proteomics and found that alkyl-CIMSS treatment of cells robustly upregulates the cell surface density of the proteoglycan glypican-1 (GPC1). Lentiviral delivery of GPC1 overexpression and shRNA knockdown constructs reveal that the presence and absence of GPC1 independently of alkyl-CIMSS treatment significantly impact HIV-1 infection, with the effect on infection corresponding to GPC1 expression. Further, we demonstrate that the influence of GPC1 on HIV-1 infection is in part mediated by TGF-{beta} signaling. Collectively, these findings implicate a cell surface protein susceptible to alkyl-CIMSS in restricting HIV-1 infection and identify GPC1 as a novel modulator of HIV-1 infection. Author SummaryWe utilized a cell-impermeable pan-kinase tool compound, alkyl-CIMSS, to identify cell surface molecules that might be involved in viral infection. Treatment of CD4+ T cells with alkyl-CIMSS increased the expression of the cell-surface protein glypican-1, which led to an increase in early HIV reverse transcriptase products and promoted viral infection. Conversely, alkyl-CIMSS inhibited herpes simplex virus entry and infection. These findings illustrate that viruses interact with exofacial cell membrane molecules differently to promote or impede infection.

microbiology↗

Unique Binding and Stabilization Mechanisms Employed By and Engineered Into Nanobodies.

Nanobodies are single domain antibody variants that bind an antigen with the precision and affinity of a conventional antibody at only a fraction of their size. In solving the crystal structures of our nanobody-GFP complexes and compared with other available structures, we uncover mechanism that enable nanobodies to function so efficiently and effectively as single-domain antibodies. We show that unlike conventional antibodies, a nanobody repertoire maximizes sampling of their antigen surface by binding a single antigen in at least three different orientations which can be predicted by their paratope composition. We also structurally reengineering these nanobodies to improve their antigen affinity, their stability, or both - results which also revealed the strong connection between nanobody stability and affinity. We achieved this by either directly modifying the paratope, or by altering a particular region within their third framework, which is a highly conserved area that we determined plays a role in controlling nanobody stability. Our study suggests that these unique characteristics of nanobodies allow them to interact with antigens as effectively as conventional antibodies, despite their smaller size. This understanding provides methods to facilitate optimizing, humanizing and functionalizing nanobodies, thus paving the way for their utilization in diverse areas such as research, diagnostics, and therapeutic development. Significance StatementNanobodies are a unique type of antibody fragment found in select animals, containing all its antigen binding ability reduced to a single [~]15 kDa protein. There is increasing development of nanobodies for research, diagnostics, and therapeutics, yet how nanobodies function so effectively as single domain antigen binders with the precision and affinity of conventional antibodies is unclear. In this study, we present key observations to help answer this question, where one key finding is the strong relationship between nanobody stability and antigen affinity aided by the identification of a highly conserved region in nanobodies essential for maintaining nanobody stability. This region may have been retained in nanobodies in lieu of stabilizing mechanisms induced by dimerization as seen in conventional antibodies.

biochemistry↗

SARS-CoV-2 multi-antigen protein microarray for detailed characterization of antibody responses in COVID-19 patients

Antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) target multiple epitopes on different domains of the spike protein, and other SARS-CoV-2 proteins. We developed a SARS-CoV-2 multi-antigen protein microarray with the nucleocapsid, spike and its domains (S1, S2), and variants with single (D614G, E484K, N501Y) or double substitutions (N501Y/Deletion69/70), allowing a more detailed high-throughput analysis of the antibody repertoire following infection. The assay was demonstrated to be reliable and comparable to ELISA. We analyzed antibodies from 18 COVID-19 patients and 12 recovered convalescent donors. S IgG level was higher than N IgG in most of the COVID-19 patients, receptor-binding domain of S1 showed high reactivity, but no antibodies were detected against heptad repeat domain 2 of S2. Furthermore, antibodies were detected against S variants with single and double substitutions in COVID-19 patients who were infected with SARS-CoV-2 early in the pandemic. Here we demonstrated that SARS-CoV-2 multi-antigen protein microarray is a powerful tool for detailed characterization of antibody responses, with potential utility in understanding the disease progress and assessing current vaccines and therapies against evolving SARS-CoV-2.

biochemistry↗

Two point mutations in protocadherin-1 disrupt Andes hantavirus recognition and afford protection against lethal infection

Andes virus and Sin Nombre virus are the etiologic agents of severe hantavirus cardiopulmonary syndrome (HCPS) in the Americas for which no FDA-approved countermeasures are available. Protocadherin-1 (PCDH1), a cadherin-superfamily protein recently identified as a critical host factor for ANDV and SNV, represents a new antiviral target; however, its precise role remains to be elucidated. Here, we used computational and experimental approaches to delineate the binding surface of the ANDV glycoprotein complex on PCDH1s first extracellular cadherin repeat domain. Strikingly, a single amino acid residue in this PCDH1 surface influenced the host species-specificity of SNV glycoprotein-PCDH1 interaction and cell entry. Mutation of this, and a neighboring residue, substantially protected Syrian hamsters from pulmonary disease and death caused by ANDV. We conclude that PCDH1 is a bona fide entry receptor for ANDV and SNV whose direct interaction with hantavirus glycoproteins could be targeted to develop new interventions against HCPS.

microbiology↗

HVEM structures and mutants reveal distinct functions of binding to LIGHT and BTLA/CD160

HVEM is a TNF (tumor necrosis factor) receptor contributing to a broad range of immune functions involving diverse cell types. It interacts with a TNF ligand, LIGHT, and immunoglobulin (Ig) superfamily members BTLA and CD160. Assessing the functional impact of HVEM binding to specific ligands in different settings has been complicated by the multiple interactions of HVEM and HVEM binding partners. To dissect the molecular basis for multiple functions, we determined crystal structures that reveal the distinct HVEM surfaces that engage LIGHT or BTLA/CD160, including the human HVEM:LIGHT:CD160 ternary complex, with HVEM interacting simultaneously with both binding partners. Based on these structures, we generated mouse HVEM mutants that selectively recognized either the TNF or Ig ligands in vitro. Knock-in mice expressing these muteins maintain expression of all the proteins in the HVEM network, yet they demonstrate selective functions for LIGHT in the clearance of bacteria in the intestine and for the Ig ligands in the amelioration of liver inflammation.

immunology↗

The Phaeodactylum tricornutum Diaminopimelate Decarboxylase was Acquired via Horizontal Gene Transfer from Bacteria and Displays Substrate Promiscuity

Diatoms are predicted to synthesize certain amino acids within the chloroplast, including L-lysine via a diaminopimelate-dependent pathway. Herein, we report that the model diatom, Phaeodactylum tricornutum, possesses a chimeric lysine biosynthetic pathway, which coalesces bacterial and plant genes, and is terminated by a chloroplast-localized diaminopimelate decarboxylase (DAPDC, PtLYSA). We show that while RNAi ablation of PtLYSA is either synthetically lethal or concomitant with a slower growth rate, Cas9-mediated mutagenesis of PtLYSA results in recovery of heterozygous cells lines, suggesting that PtLYSA is an essential gene. Previously characterized DAPDCs are unique within the PLP-dependent decarboxylases where catalysis occurs at the D-stereocenter of the substrate and display a strict stereochemical preference for a (D,L)- or meso-substrate and not the D,D- or L,L-isomers of diaminopimelate (DAP) to synthesize L-lysine. Using decarboxylation assays and differential scanning calorimetry analyses, we validate that PtLYSA is a bona fide DAPDC and uncover its unexpected stereopromiscuous behavior in substrate specificity. The crystal structure of PtLYSA confirms the enzyme is an obligate homodimer in which both protomers reciprocally participate in the active site. The structure underscores features unique to the PtLYSA clan of DAPDC and provides structural insight into the determinants responsible for the substrate-promiscuity observed in PtLYSA.

biochemistry↗

Signatures and mechanisms of efficacious therapeutic ribonucleotides against SARS-CoV-2 revealed by analysis of its replicase using magnetic tweezers

The nucleotide analog Remdesivir (RDV) is the only FDA-approved antiviral therapy to treat infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The physical basis for efficient utilization of RDV by SARS-CoV-2 polymerase is unknown. Here, we characterize the impact of RDV and other nucleotide analogs on RNA synthesis by the polymerase using a high-throughput, single-molecule, magnetic-tweezers platform. The location of the modification in the ribose or in the base dictates the catalytic pathway(s) used for its incorporation. We reveal that RDV incorporation does not terminate viral RNA synthesis, but leads the polymerase into deep backtrack, which may appear as termination in traditional ensemble assays. SARS-CoV-2 is able to evade the endogenously synthesized product of the viperin antiviral protein, ddhCTP, though the polymerase incorporates this nucleotide analog well. This experimental paradigm is essential to the discovery and development of therapeutics targeting viral polymerases. TeaserWe revise Remdesivirs mechanism of action and reveal SARS-CoV-2 ability to evade interferon-induced antiviral ddhCTP

biophysics↗

Characterization of the SARS-CoV-2 S Protein: Biophysical, Biochemical, Structural, and Antigenic Analysis

Coronavirus disease 2019 (COVID-19) is a global health crisis caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and there is a critical need to produce large quantities of high-quality SARS-CoV-2 Spike (S) protein for use in both clinical and basic science settings. To address this need, we have evaluated the expression and purification of two previously reported S protein constructs in Expi293F and ExpiCHO-S cells, two different cell lines selected for increased expression of secreted glycoproteins. We show that ExpiCHO-S cells produce enhanced yields of both SARS-CoV-2 S proteins. Biochemical, biophysical, and structural (cryo-EM) characterization of the SARS-CoV-2 S proteins produced in both cell lines demonstrate that the reported purification strategy yields high quality S protein (non-aggregated, uniform material with appropriate biochemical and biophysical properties). Importantly, we show that multiple preparations of these two recombinant S proteins from either cell line exhibit identical behavior in two different serology assays. We also evaluate the specificity of S protein-mediated host cell binding by examining interactions with proposed binding partners in the human secretome. In addition, the antigenicity of these proteins is demonstrated by standard ELISAs, and in a flexible protein microarray format. Collectively, we establish an array of metrics for ensuring the production of high-quality S protein to support clinical, biological, biochemical, structural and mechanistic studies to combat the global pandemic caused by SARS-CoV-2.

biochemistry↗

Structure of a Single Chain H2A/H2B Dimer

Chromatin is the complex assembly of nucleic acids and proteins that makes up the physiological form of the eukaryotic genome. The nucleosome is the fundamental repeating unit of chromatin, composed of ~147bp of DNA wrapped around a histone octamer formed by two copies of each core histone: H2A, H2B, H3 and H4. Prior to nucleosome assembly, and during histone eviction, histones are typically assembled into soluble H2A/H2B dimers and H3/H4 dimers and tetramers. A multitude of factors interact with soluble histone dimers and tetramers, including chaperones, importins, histone modifying enzymes, and chromatin remodeling enzymes. It is still unclear how many of these proteins recognize soluble histones; therefore, there is a need for new structural tools to study non-nucleosomal histones. Here we created a single-chain, tailless Xenopus H2A/H2B dimer by directly fusing the C-terminus of H2B to the N-terminus of H2A. We show that this construct (termed scH2BH2A) is readily expressed in bacteria and can be purified under non-denaturing conditions. A 1.31[A] crystal structure of scH2BH2A shows that it adopts a conformation nearly identical to nucleosomal H2A/H2B. This new tool will facilitate future structural studies of a multitude of H2A/H2B-interacting proteins.

biochemistry↗

A binary arginine methylation switch on histone H3 Arginine 2 regulates its interaction with WDR5

Histone H3 arginine 2 (H3R2) is post-translationally modified in three different states by "writers" of the protein arginine methyltransferase (PRMT) family. H3R2 methylarginine isoforms include PRMT5-catalyzed mono- and symmetric di-methylation (me1, me2s), and PRMT6-catalyzed me1 and asymmetric dimethylation (me2a). WD-40 repeat-containing protein 5 (WDR5) is an epigenetic "reader" protein that interacts with H3R2 and is a subunit of numerous chromatin-modifying complexes, such as the Mixed Lineage Leukemia (MLL) H3 lysine 4 methyltransferase complex. Previous studies suggested that MLL recruitment to chromatin was specified by the high-affinity interaction between WDR5 and H3R2me2s. However, our prior biological data prompted the hypothesis that WDR5 may also interact with H3R2me1 to recruit MLL activity. Here, using highly accurate quantitative binding analysis combined with high-resolution crystal structures of WDR5 in complex with unmodified (me0) and me1/me2s L-Arginine amino acids and in complex with H3R2me1 peptide, we provide a rigorous biochemical study of this important biological interaction. Despite modest structural differences at the binding interface, our study supports an interaction model regulated by a binary arginine methylation switch: H3R2me2a prevents interaction with WDR5, whereas H3R2me0/me1/me2s are equally permissive.

biochemistry↗

Discovery of a novel stereospecific β-hydroxyacyl-CoA lyase/thioesterase shared by three metabolic pathways in Mycobacterium tuberculosis

The vast number of poorly characterised enzymes in Mycobacterium tuberculosis (Mtb) is one of the key barriers precluding a better understanding of the biology that underpins pathogenesis. Here, we investigated the Mtb orphan enzyme Rv2498c to delineate its physiological role. Our results from in vitro enzymatic assays, phylogenetic analysis, X-ray crystallography and in vivo Mtb experiments, de-orphan Rv2498c as a multi-functional {beta}-hydroxyacyl-CoA lyase/thioesterase ({beta}-HAClyase/thioesterase) that participates in three different metabolic pathways: L-leucine catabolism, itaconate dissimilation, and glyoxylate shunt. Moreover, the deletion of the rv2498c gene from the Mtb genome resulted in attenuation in the mouse model compared to infection with the parent strain. To the best of our knowledge, this is the first report of an (R)-3-hydroxyl-3-methylglutaryl-CoA for leucine catabolism and an itaconate-specific resistance mechanism in Mtb.

biochemistry↗