NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction

<p>Abstract</p> <p>Background</p> <p>Nuclear localization signals (NLSs) are stretches of residues within a protein that are important for the regulated nuclear import of the protein. Of the many import pathways that exist in yeast, the best characterized is termed the 'classical' NLS pathway. The classical NLS contains specific patterns of basic residues and computational methods have been designed to predict the location of these motifs on proteins. The consensus sequences, or patterns, for the other import pathways are less well-understood.</p> <p>Results</p> <p>In this paper, we present an analysis of characterized NLSs in yeast, and find, despite the large number of nuclear import pathways, that NLSs seem to show similar patterns of amino acid residues. We test current prediction methods and observe a low true positive rate. We therefore suggest an approach using hidden Markov models (HMMs) to predict novel NLSs in proteins. We show that our method is able to consistently find 37% of the NLSs with a low false positive rate and that our method retains its true positive rate outside of the yeast data set used for the training parameters.</p> <p>Conclusion</p> <p>Our implementation of this model, NLStradamus, is made available at: <url>http://www.moseslab.csb.utoronto.ca/NLStradamus/</url></p

Investigation of the Immunogenicity and Specificity of the Transferrin Binding Proteins from Bovine Pathogenic Bacteria

Through trying to survive and proliferate within their hosts, pathogens have developed creative mechanisms of acquiring iron. A nutrient required for survival by most organisms, iron is both highly sought and jealously guarded. Hosts sequester iron using iron-binding proteins. These iron sinks keep the extracellular concentration of free iron at a level that does not support microbial proliferation. Transferrin is a bilobal iron carrying protein found in the blood and cerebrospinal fluid, and on mucosal surfaces. It is targeted by a number of microbial transferrin binding proteins and siderophores. This thesis focuses on one of the best-studied bacterial transferrin receptors, which consists of the transporter TbpA and its associated surface lipoprotein TbpB. TbpA and TbpB have been studied for years as potential vaccine antigens. Recently, mutants of TbpB that do not bind transferrin have been shown to provide improved protection against infection compared to wild-type TbpB. In this thesis, I develop a method for rapidly screening TbpB mutants, measure loss of affinity for multiple mutations, and investigate the effectiveness of a mutant in generating transferrin blocking antibodies. Furthermore, I investigate multiple methods of measuring binding specificity in Tbp-transferrin interactions in order to lay the groundwork for identifying functionally important residues in Tbps, and for designing improved animal models of infection.Ph.D.2021-11-14 00:00:0

Lactoferrin binding protein B – a bi-functional bacterial receptor protein

<div><p>Lactoferrin binding protein B (LbpB) is a bi-lobed outer membrane-bound lipoprotein that comprises part of the lactoferrin (Lf) receptor complex in <i>Neisseria meningitidis</i> and other Gram-negative pathogens. Recent studies have demonstrated that LbpB plays a role in protecting the bacteria from cationic antimicrobial peptides due to large regions rich in anionic residues in the C-terminal lobe. Relative to its homolog, transferrin-binding protein B (TbpB), there currently is little evidence for its role in iron acquisition and relatively little structural and biophysical information on its interaction with Lf. In this study, a combination of crosslinking and deuterium exchange coupled to mass spectrometry, information-driven computational docking, bio-layer interferometry, and site-directed mutagenesis was used to probe LbpB:hLf complexes. The formation of a 1:1 complex of iron-loaded Lf and LbpB involves an interaction between the Lf C-lobe and LbpB N-lobe, comparable to TbpB, consistent with a potential role in iron acquisition. The Lf N-lobe is also capable of binding to negatively charged regions of the LbpB C-lobe and possibly other sites such that a variety of higher order complexes are formed. Our results are consistent with LbpB serving dual roles focused primarily on iron acquisition when exposed to limited levels of iron-loaded Lf on the mucosal surface and effectively binding apo Lf when exposed to high levels at sites of inflammation.</p></div

LbpB mutants.

<p>LbpB mutants.</p

Proposed functions of LbpB.

<p>(LEFT) LbpB may be involved in the iron-acquisition pathway. At low concentrations of holo-hLf, LbpB may use its LbpB-N binding mode to preferentially bind iron-loaded lactoferrin and shuttle it to LbpA, forming a ternary complex and hijacking the iron. (RIGHT) Cleavage of LbpB from the membrane may be dependent on the presence of high levels of hLf in the extracellular milieu or simply a constitutive property of <i>N</i>. <i>meningitidis</i> cells in the NalP phase-variable ON-state. The release of LbpB from the membrane is done in an effort to sequester lactoferricin, antibodies, and possibly form large lattices of hLf as to prevent proteolytical processing into its derivative cationic antimicrobial peptides.</p

Receptor lobe binding contributions in TbpB and LbpB.

<p>Cartoon representations of each recombinant LbpB protein are displayed beside their respective BLI steady-state binding curve from binding hLf. (A) Intact LbpB, K_{D app} = 72.8 ± 3.24nM. (B) LbpB-N lobe, K_{D app} = 126 ± 48nM. (C) LbpB-C lobe K_{D app} = 279 ± 15nM. C-lobe Hill slope was calculated to be 1.98 ± 0.13 implying positive cooperativity. (D) Intact-lgsm, K_{D app} = 140 ±82.4nM (E). LbpB-C lobe-lgsm had no observed binding.</p

Specificity of LbpB and TbpB for iron-loaded glycoprotein.

<p>(A) Competitive solid-phase binding assay of TbpB with apo/holo hTf and LbpB with apo/holo hLf. Recombinant MBP-TbpB (top two rows) and MBP-LbpB (bottom two rows) were applied to nitrocellulose paper, the paper blocked and then incubated with apo- or holo- glycoprotein overnight in a ¼ serially diluted fashion (A, 20nM; B, 5nM; C, 1.25nM; D, 0.31nM; E, 0.07nM; F, 0.01nM; G, 4.88 × 10^-3nM; H, 0nM). Iron-loaded HRP-conjugated glycoprotein (HRP-hTf or HRP-hLf) was then introduced into the binding mixture. Presence of a dot represents the displacement of any protein bound to TbpB or LbpB by the HRP-conjugate at the given concentration. (B) SDS-PAGE/affinity capture representing receptor protein (MBP-TbpB, 122kDa; or MBP-LbpB, 122kDa) captured by Sepharose resins conjugated to their cognate apo- or holo-glycoprotein (hTf-r, hLf-r).</p

Global BioID-based SARS-CoV-2 proteins proximal interactome unveils novel ties between viral polypeptides and host factors involved in multiple COVID19-associated mechanisms

The worldwide SARS-CoV-2 outbreak poses a serious challenge to human societies and economies. SARS-CoV-2 proteins orchestrate complex pathogenic mechanisms that underlie COVID-19 disease. Thus, understanding how viral polypeptides rewire host protein networks enables better-founded therapeutic research. In complement to existing proteomic studies, in this study we define the first proximal interaction network of SARS-CoV-2 proteins, at the whole proteome level in human cells. Applying a proximity-dependent biotinylation (BioID)-based approach greatly expanded the current knowledge by detecting interactions within poorly soluble compartments, transient, and/or of weak affinity in living cells. Our BioID study was complemented by a stringent filtering and uncovered 2,128 unique cellular targets (1,717 not previously associated with SARS-CoV-1 or 2 proteins) connected to the N- and C-ter BioID-tagged 28 SARS-CoV-2 proteins by a total of 5,415 (5,236 new) proximal interactions. In order to facilitate data exploitation, an innovative interactive 3D web interface was developed to allow customized analysis and exploration of the landscape of interactions (accessible at http://www.sars-cov-2-interactome.org/ ). Interestingly, 342 membrane proteins including interferon and interleukin pathways factors, were associated with specific viral proteins. We uncovered ORF7a and ORF7b protein proximal partners that could be related to anosmia and ageusia symptoms. Moreover, comparing proximal interactomes in basal and infection-mimicking conditions (poly(I:C) treatment) allowed us to detect novel links with major antiviral response pathway components, such as ORF9b with MAVS and ISG20; N with PKR and TARB2; NSP2 with RIG-I and STAT1; NSP16 with PARP9-DTX3L. Altogether, our study provides an unprecedented comprehensive resource for understanding how SARS-CoV-2 proteins orchestrate host proteome remodeling and innate immune response evasion, which can inform development of targeted therapeutic strategies