Publications by authors named "Laura E Rosen"

21 Publications

  • Page 1 of 1

Broad sarbecovirus neutralization by a human monoclonal antibody.

Nature 2021 09 19;597(7874):103-108. Epub 2021 Jul 19.

Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland.

The recent emergence of SARS-CoV-2 variants of concern and the recurrent spillovers of coronaviruses into the human population highlight the need for broadly neutralizing antibodies that are not affected by the ongoing antigenic drift and that can prevent or treat future zoonotic infections. Here we describe a human monoclonal antibody designated S2X259, which recognizes a highly conserved cryptic epitope of the receptor-binding domain and cross-reacts with spikes from all clades of sarbecovirus. S2X259 broadly neutralizes spike-mediated cell entry of SARS-CoV-2, including variants of concern (B.1.1.7, B.1.351, P.1, and B.1.427/B.1.429), as well as a wide spectrum of human and potentially zoonotic sarbecoviruses through inhibition of angiotensin-converting enzyme 2 (ACE2) binding to the receptor-binding domain. Furthermore, deep-mutational scanning and in vitro escape selection experiments demonstrate that S2X259 possesses an escape profile that is limited to a single substitution, G504D. We show that prophylactic and therapeutic administration of S2X259 protects Syrian hamsters (Mesocricetus auratus) against challenge with the prototypic SARS-CoV-2 and the B.1.351 variant of concern, which suggests that this monoclonal antibody is a promising candidate for the prevention and treatment of emergent variants and zoonotic infections. Our data reveal a key antigenic site that is targeted by broadly neutralizing antibodies and will guide the design of vaccines that are effective against all sarbecoviruses.
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http://dx.doi.org/10.1038/s41586-021-03817-4DOI Listing
September 2021

SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape.

Nature 2021 09 14;597(7874):97-102. Epub 2021 Jul 14.

Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland.

An ideal therapeutic anti-SARS-CoV-2 antibody would resist viral escape, have activity against diverse sarbecoviruses, and be highly protective through viral neutralization and effector functions. Understanding how these properties relate to each other and vary across epitopes would aid the development of therapeutic antibodies and guide vaccine design. Here we comprehensively characterize escape, breadth and potency across a panel of SARS-CoV-2 antibodies targeting the receptor-binding domain (RBD). Despite a trade-off between in vitro neutralization potency and breadth of sarbecovirus binding, we identify neutralizing antibodies with exceptional sarbecovirus breadth and a corresponding resistance to SARS-CoV-2 escape. One of these antibodies, S2H97, binds with high affinity across all sarbecovirus clades to a cryptic epitope and prophylactically protects hamsters from viral challenge. Antibodies that target the angiotensin-converting enzyme 2 (ACE2) receptor-binding motif (RBM) typically have poor breadth and are readily escaped by mutations despite high neutralization potency. Nevertheless, we also characterize a potent RBM antibody (S2E12) with breadth across sarbecoviruses related to SARS-CoV-2 and a high barrier to viral escape. These data highlight principles underlying variation in escape, breadth and potency among antibodies that target the RBD, and identify epitopes and features to prioritize for therapeutic development against the current and potential future pandemics.
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http://dx.doi.org/10.1038/s41586-021-03807-6DOI Listing
September 2021

SARS-CoV-2 immune evasion by the B.1.427/B.1.429 variant of concern.

Science 2021 08 1;373(6555):648-654. Epub 2021 Jul 1.

Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland.

A novel variant of concern (VOC) named CAL.20C (B.1.427/B.1.429), which was originally detected in California, carries spike glycoprotein mutations S13I in the signal peptide, W152C in the N-terminal domain (NTD), and L452R in the receptor-binding domain (RBD). Plasma from individuals vaccinated with a Wuhan-1 isolate-based messenger RNA vaccine or from convalescent individuals exhibited neutralizing titers that were reduced 2- to 3.5-fold against the B.1.427/B.1.429 variant relative to wild-type pseudoviruses. The L452R mutation reduced neutralizing activity in 14 of 34 RBD-specific monoclonal antibodies (mAbs). The S13I and W152C mutations resulted in total loss of neutralization for 10 of 10 NTD-specific mAbs because the NTD antigenic supersite was remodeled by a shift of the signal peptide cleavage site and the formation of a new disulfide bond, as revealed by mass spectrometry and structural studies.
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http://dx.doi.org/10.1126/science.abi7994DOI Listing
August 2021

Structural basis for broad sarbecovirus neutralization by a human monoclonal antibody.

bioRxiv 2021 Apr 8. Epub 2021 Apr 8.

Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland.

The recent emergence of SARS-CoV-2 variants of concern (VOC) and the recurrent spillovers of coronaviruses in the human population highlight the need for broadly neutralizing antibodies that are not affected by the ongoing antigenic drift and that can prevent or treat future zoonotic infections. Here, we describe a human monoclonal antibody (mAb), designated S2×259, recognizing a highly conserved cryptic receptor-binding domain (RBD) epitope and cross-reacting with spikes from all sarbecovirus clades. S2×259 broadly neutralizes spike-mediated entry of SARS-CoV-2 including the B.1.1.7, B.1.351, P.1 and B.1.427/B.1.429 VOC, as well as a wide spectrum of human and zoonotic sarbecoviruses through inhibition of ACE2 binding to the RBD. Furthermore, deep-mutational scanning and escape selection experiments demonstrate that S2×259 possesses a remarkably high barrier to the emergence of resistance mutants. We show that prophylactic administration of S2×259 protects Syrian hamsters against challenges with the prototypic SARS-CoV-2 and the B.1.351 variant, suggesting this mAb is a promising candidate for the prevention and treatment of emergent VOC and zoonotic infections. Our data unveil a key antigenic site targeted by broadly-neutralizing antibodies and will guide the design of pan-sarbecovirus vaccines.
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http://dx.doi.org/10.1101/2021.04.07.438818DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8043460PMC
April 2021

Antibodies to the SARS-CoV-2 receptor-binding domain that maximize breadth and resistance to viral escape.

bioRxiv 2021 Apr 8. Epub 2021 Apr 8.

Vir Biotechnology, San Francisco, CA 94158, USA.

An ideal anti-SARS-CoV-2 antibody would resist viral escape , have activity against diverse SARS-related coronaviruses , and be highly protective through viral neutralization and effector functions . Understanding how these properties relate to each other and vary across epitopes would aid development of antibody therapeutics and guide vaccine design. Here, we comprehensively characterize escape, breadth, and potency across a panel of SARS-CoV-2 antibodies targeting the receptor-binding domain (RBD), including S309 , the parental antibody of the late-stage clinical antibody VIR-7831. We observe a tradeoff between SARS-CoV-2 neutralization potency and breadth of binding across SARS-related coronaviruses. Nevertheless, we identify several neutralizing antibodies with exceptional breadth and resistance to escape, including a new antibody (S2H97) that binds with high affinity to all SARS-related coronavirus clades via a unique RBD epitope centered on residue E516. S2H97 and other escape-resistant antibodies have high binding affinity and target functionally constrained RBD residues. We find that antibodies targeting the ACE2 receptor binding motif (RBM) typically have poor breadth and are readily escaped by mutations despite high neutralization potency, but we identify one potent RBM antibody (S2E12) with breadth across sarbecoviruses closely related to SARS-CoV-2 and with a high barrier to viral escape. These data highlight functional diversity among antibodies targeting the RBD and identify epitopes and features to prioritize for antibody and vaccine development against the current and potential future pandemics.
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http://dx.doi.org/10.1101/2021.04.06.438709DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8043444PMC
April 2021

SARS-CoV-2 immune evasion by variant B.1.427/B.1.429.

bioRxiv 2021 Apr 1. Epub 2021 Apr 1.

SARS-CoV-2 entry is mediated by the spike (S) glycoprotein which contains the receptor-binding domain (RBD) and the N-terminal domain (NTD) as the two main targets of neutralizing antibodies (Abs). A novel variant of concern (VOC) named CAL.20C (B.1.427/B.1.429) was originally detected in California and is currently spreading throughout the US and 29 additional countries. It is unclear whether antibody responses to SARS-CoV-2 infection or to the prototypic Wuhan-1 isolate-based vaccines will be impacted by the three B.1.427/B.1.429 S mutations: S13I, W152C and L452R. Here, we assessed neutralizing Ab responses following natural infection or mRNA vaccination using pseudoviruses expressing the wildtype or the B.1.427/B.1.429 S protein. Plasma from vaccinated or convalescent individuals exhibited neutralizing titers, which were reduced 3-6 fold against the B.1.427/B.1.429 variant relative to wildtype pseudoviruses. The RBD L452R mutation reduced or abolished neutralizing activity of 14 out of 35 RBD-specific monoclonal antibodies (mAbs), including three clinical-stage mAbs. Furthermore, we observed a complete loss of B.1.427/B.1.429 neutralization for a panel of mAbs targeting the N-terminal domain due to a large structural rearrangement of the NTD antigenic supersite involving an S13I-mediated shift of the signal peptide cleavage site. These data warrant closer monitoring of signal peptide variants and their involvement in immune evasion and show that Abs directed to the NTD impose a selection pressure driving SARS-CoV-2 viral evolution through conventional and unconventional escape mechanisms.
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http://dx.doi.org/10.1101/2021.03.31.437925DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8020983PMC
April 2021

N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2.

Cell 2021 04 16;184(9):2332-2347.e16. Epub 2021 Mar 16.

Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA.

The SARS-CoV-2 spike (S) glycoprotein contains an immunodominant receptor-binding domain (RBD) targeted by most neutralizing antibodies (Abs) in COVID-19 patient plasma. Little is known about neutralizing Abs binding to epitopes outside the RBD and their contribution to protection. Here, we describe 41 human monoclonal Abs (mAbs) derived from memory B cells, which recognize the SARS-CoV-2 S N-terminal domain (NTD) and show that a subset of them neutralize SARS-CoV-2 ultrapotently. We define an antigenic map of the SARS-CoV-2 NTD and identify a supersite (designated site i) recognized by all known NTD-specific neutralizing mAbs. These mAbs inhibit cell-to-cell fusion, activate effector functions, and protect Syrian hamsters from SARS-CoV-2 challenge, albeit selecting escape mutants in some animals. Indeed, several SARS-CoV-2 variants, including the B.1.1.7, B.1.351, and P.1 lineages, harbor frequent mutations within the NTD supersite, suggesting ongoing selective pressure and the importance of NTD-specific neutralizing mAbs for protective immunity and vaccine design.
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http://dx.doi.org/10.1016/j.cell.2021.03.028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7962585PMC
April 2021

Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity.

Cell 2021 03 28;184(5):1171-1187.e20. Epub 2021 Jan 28.

MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow G61 1QH, UK.

SARS-CoV-2 can mutate and evade immunity, with consequences for efficacy of emerging vaccines and antibody therapeutics. Here, we demonstrate that the immunodominant SARS-CoV-2 spike (S) receptor binding motif (RBM) is a highly variable region of S and provide epidemiological, clinical, and molecular characterization of a prevalent, sentinel RBM mutation, N439K. We demonstrate N439K S protein has enhanced binding affinity to the hACE2 receptor, and N439K viruses have similar in vitro replication fitness and cause infections with similar clinical outcomes as compared to wild type. We show the N439K mutation confers resistance against several neutralizing monoclonal antibodies, including one authorized for emergency use by the US Food and Drug Administration (FDA), and reduces the activity of some polyclonal sera from persons recovered from infection. Immune evasion mutations that maintain virulence and fitness such as N439K can emerge within SARS-CoV-2 S, highlighting the need for ongoing molecular surveillance to guide development and usage of vaccines and therapeutics.
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http://dx.doi.org/10.1016/j.cell.2021.01.037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7843029PMC
March 2021

N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2.

bioRxiv 2021 Jan 14. Epub 2021 Jan 14.

SARS-CoV-2 entry into host cells is orchestrated by the spike (S) glycoprotein that contains an immunodominant receptor-binding domain (RBD) targeted by the largest fraction of neutralizing antibodies (Abs) in COVID-19 patient plasma. Little is known about neutralizing Abs binding to epitopes outside the RBD and their contribution to protection. Here, we describe 41 human monoclonal Abs (mAbs) derived from memory B cells, which recognize the SARS-CoV-2 S N-terminal domain (NTD) and show that a subset of them neutralize SARS-CoV-2 ultrapotently. We define an antigenic map of the SARS-CoV-2 NTD and identify a supersite recognized by all known NTD-specific neutralizing mAbs. These mAbs inhibit cell-to-cell fusion, activate effector functions, and protect Syrian hamsters from SARS-CoV-2 challenge. SARS-CoV-2 variants, including the 501Y.V2 and B.1.1.7 lineages, harbor frequent mutations localized in the NTD supersite suggesting ongoing selective pressure and the importance of NTD-specific neutralizing mAbs to protective immunity.
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http://dx.doi.org/10.1101/2021.01.14.426475DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7814825PMC
January 2021

Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology.

Cell 2020 11 16;183(4):1024-1042.e21. Epub 2020 Sep 16.

III Division of Infectious Diseases, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, 20157 Milan, Italy.

Analysis of the specificity and kinetics of neutralizing antibodies (nAbs) elicited by SARS-CoV-2 infection is crucial for understanding immune protection and identifying targets for vaccine design. In a cohort of 647 SARS-CoV-2-infected subjects, we found that both the magnitude of Ab responses to SARS-CoV-2 spike (S) and nucleoprotein and nAb titers correlate with clinical scores. The receptor-binding domain (RBD) is immunodominant and the target of 90% of the neutralizing activity present in SARS-CoV-2 immune sera. Whereas overall RBD-specific serum IgG titers waned with a half-life of 49 days, nAb titers and avidity increased over time for some individuals, consistent with affinity maturation. We structurally defined an RBD antigenic map and serologically quantified serum Abs specific for distinct RBD epitopes leading to the identification of two major receptor-binding motif antigenic sites. Our results explain the immunodominance of the receptor-binding motif and will guide the design of COVID-19 vaccines and therapeutics.
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http://dx.doi.org/10.1016/j.cell.2020.09.037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7494283PMC
November 2020

Ultrapotent human antibodies protect against SARS-CoV-2 challenge via multiple mechanisms.

Science 2020 11 24;370(6519):950-957. Epub 2020 Sep 24.

Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland.

Efficient therapeutic options are needed to control the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that has caused more than 922,000 fatalities as of 13 September 2020. We report the isolation and characterization of two ultrapotent SARS-CoV-2 human neutralizing antibodies (S2E12 and S2M11) that protect hamsters against SARS-CoV-2 challenge. Cryo-electron microscopy structures show that S2E12 and S2M11 competitively block angiotensin-converting enzyme 2 (ACE2) attachment and that S2M11 also locks the spike in a closed conformation by recognition of a quaternary epitope spanning two adjacent receptor-binding domains. Antibody cocktails that include S2M11, S2E12, or the previously identified S309 antibody broadly neutralize a panel of circulating SARS-CoV-2 isolates and activate effector functions. Our results pave the way to implement antibody cocktails for prophylaxis or therapy, circumventing or limiting the emergence of viral escape mutants.
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http://dx.doi.org/10.1126/science.abe3354DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7857395PMC
November 2020

Cohesin cleavage by separase is enhanced by a substrate motif distinct from the cleavage site.

Nat Commun 2019 11 15;10(1):5189. Epub 2019 Nov 15.

Department of Physiology, University of California, San Francisco, CA, 94143, USA.

Chromosome segregation begins when the cysteine protease, separase, cleaves the Scc1 subunit of cohesin at the metaphase-to-anaphase transition. Separase is inhibited prior to metaphase by the tightly bound securin protein, which contains a pseudosubstrate motif that blocks the separase active site. To investigate separase substrate specificity and regulation, here we develop a system for producing recombinant, securin-free human separase. Using this enzyme, we identify an LPE motif on the Scc1 substrate that is distinct from the cleavage site and is required for rapid and specific substrate cleavage. Securin also contains a conserved LPE motif, and we provide evidence that this sequence blocks separase engagement of the Scc1 LPE motif. Our results suggest that rapid cohesin cleavage by separase requires a substrate docking interaction outside the active site. This interaction is blocked by securin, providing a second mechanism by which securin inhibits cohesin cleavage.
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http://dx.doi.org/10.1038/s41467-019-13209-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6858450PMC
November 2019

SURVEY OF ANTITUBERCULOSIS DRUG ADMINISTRATION AND ADVERSE EFFECTS IN ELEPHANTS IN NORTH AMERICA.

J Zoo Wildl Med 2019 03;50(1):23-32

South African Medical Research Council Centre for TB Research, Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 8000, South Africa.

Tuberculosis, caused by , is a disease causing morbidity and mortality in captive elephants ( and ) as well as free-ranging individuals. Elephants in North America diagnosed with tuberculosis are often treated with antituberculosis drugs, unlike livestock species, which has necessitated the development of treatment guidelines adapted from recommendations for humans. There are few published reports describing empirical treatment, which may be complicated by poor patient compliance, interruptions in drug administration, and adverse effects. A survey of elephants in North America was conducted to compile information on treatment protocols, including drugs, dosages, routes of administration, serum drug concentrations, and adverse effects of antituberculosis treatment. Responses were received regarding 182 elephants, 12 of which were treated prophylactically or therapeutically with antituberculosis drugs. Treatment protocols varied among elephants, and included various combinations of isoniazid, rifampin, pyrazinamide, ethambutol, enrofloxacin, levofloxacin, and ethionamide. Serum drug concentrations also varied considerably among and within individuals. Facility staff reported 5 elephants (out of 7 treated elephants with responses) that exhibited clinical signs that may have been associated with antituberculosis drugs or treatment procedures. Anorexia, decreased water intake, constipation, depression, ataxia, limb paresis, and tremors were among the signs observed. Most adverse effects were reported to be moderate or severe, resulting in interruption of the treatment. The results from this survey provide veterinarians and elephant managers with valuable historical data to make informed clinical management decisions regarding antituberculosis therapy in elephants.
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http://dx.doi.org/10.1638/2018-0028DOI Listing
March 2019

Autonomously folding protein fragments reveal differences in the energy landscapes of homologous RNases H.

PLoS One 2015 24;10(3):e0119640. Epub 2015 Mar 24.

Biophysics Graduate Group, University of California, Berkeley, CA, United States of America; California Institute for Quantitative Biosciences - Berkeley, Berkeley, CA, United States of America; Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States of America.

An important approach to understanding how a protein sequence encodes its energy landscape is to compare proteins with different sequences that fold to the same general native structure. In this work, we compare E. coli and T. thermophilus homologs of the protein RNase H. Using protein fragments, we create equilibrium mimics of two different potential partially-folded intermediates (I(core) and I(core+1)) hypothesized to be present on the energy landscapes of these two proteins. We observe that both T. thermophilus RNase H (ttRNH) fragments are folded and have distinct stabilities, indicating that both regions are capable of autonomous folding and that both intermediates are present as local minima on the ttRNH energy landscape. In contrast, the two E. coli RNase H (ecRNH) fragments have very similar stabilities, suggesting that the presence of additional residues in the I(core+1) fragment does not affect the folding or structure as compared to I(core). NMR experiments provide additional evidence that only the I(core) intermediate is populated by ecRNH. This is one of the biggest differences that has been observed between the energy landscapes of these two proteins. Additionally, we used a FRET experiment in the background of full-length ttRNH to specifically monitor the formation of the I(core+1) intermediate. We determine that the ttRNH I(core+1) intermediate is likely the intermediate populated prior to the rate-limiting barrier to global folding, in contrast to E. coli RNase H for which I(core) is the folding intermediate. This result provides new insight into the nature of the rate-limiting barrier for the folding of RNase H.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0119640PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4372590PMC
February 2016

Non-native structure appears in microseconds during the folding of E. coli RNase H.

J Mol Biol 2015 Jan 13;427(2):443-53. Epub 2014 Oct 13.

Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3220, USA; California Institute for Quantitative Biosciences-Berkeley, University of California, Berkeley, Berkeley, CA 94720-3220, USA; Department of Molecular and Cell Biology-Berkeley, University of California, Berkeley, Berkeley, CA 94720-3220, USA. Electronic address:

The folding pathway of Escherichia coli RNase H is one of the best experimentally characterized for any protein. In spite of this, spectroscopic studies have never captured the earliest events. Using continuous-flow microfluidic mixing, we have now observed the first several milliseconds of folding by monitoring the tryptophan fluorescence lifetime (60 μs dead time). Two folding intermediates are observed, the second of which is the previously characterized I(core) millisecond intermediate. The new earlier intermediate is likely on-pathway and appears to have long-range non-native structure, providing a rare example of such non-native structure formation in a folding pathway. The tryptophan fluorescence lifetimes also suggest a deviation from native packing in the second intermediate, I(core). Similar results from a fragment of RNase H demonstrate that only half of the protein is significantly involved in this early structure formation. These studies give us a view of the formation of tertiary structure on the folding pathway, which complements previous hydrogen-exchange studies that monitored only secondary structure and observed sequential native structure formation. Our results provide detailed folding information on both a timescale and a size-scale accessible to all-atom molecular dynamics simulations of protein folding.
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http://dx.doi.org/10.1016/j.jmb.2014.10.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4624390PMC
January 2015

Evidence for close side-chain packing in an early protein folding intermediate previously assumed to be a molten globule.

Proc Natl Acad Sci U S A 2014 Oct 25;111(41):14746-51. Epub 2014 Sep 25.

Biophysics Graduate Group, Institute for Quantitative Biosciences-Berkeley, University of California, Berkeley, CA 94720-3220 Chemical Biology Graduate Program, Department of Molecular and Cell Biology, and

The molten globule, a conformational ensemble with significant secondary structure but only loosely packed tertiary structure, has been suggested to be a ubiquitous intermediate in protein folding. However, it is difficult to assess the tertiary packing of transiently populated species to evaluate this hypothesis. Escherichia coli RNase H is known to populate an intermediate before the rate-limiting barrier to folding that has long been thought to be a molten globule. We investigated this hypothesis by making mimics of the intermediate that are the ground-state conformation at equilibrium, using two approaches: a truncation to generate a fragment mimic of the intermediate, and selective destabilization of the native state using point mutations. Spectroscopic characterization and the response of the mimics to further mutation are consistent with studies on the transient kinetic intermediate, indicating that they model the early intermediate. Both mimics fold cooperatively and exhibit NMR spectra indicative of a closely packed conformation, in contrast to the hypothesis of molten tertiary packing. This result is important for understanding the nature of the subsequent rate-limiting barrier to folding and has implications for the assumption that many other proteins populate molten globule folding intermediates.
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http://dx.doi.org/10.1073/pnas.1410630111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4205613PMC
October 2014

Stepwise protein folding at near amino acid resolution by hydrogen exchange and mass spectrometry.

Proc Natl Acad Sci U S A 2013 May 19;110(19):7684-9. Epub 2013 Apr 19.

Johnson Research Foundation, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

The kinetic folding of ribonuclease H was studied by hydrogen exchange (HX) pulse labeling with analysis by an advanced fragment separation mass spectrometry technology. The results show that folding proceeds through distinct intermediates in a stepwise pathway that sequentially incorporates cooperative native-like structural elements to build the native protein. Each step is seen as a concerted transition of one or more segments from an HX-unprotected to an HX-protected state. Deconvolution of the data to near amino acid resolution shows that each step corresponds to the folding of a secondary structural element of the native protein, termed a "foldon." Each folded segment is retained through subsequent steps of foldon addition, revealing a stepwise buildup of the native structure via a single dominant pathway. Analysis of the pertinent literature suggests that this model is consistent with experimental results for many proteins and some current theoretical results. Two biophysical principles appear to dictate this behavior. The principle of cooperativity determines the central role of native-like foldon units. An interaction principle termed "sequential stabilization" based on native-like interfoldon interactions orders the pathway.
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http://dx.doi.org/10.1073/pnas.1305887110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3651421PMC
May 2013

Detection of Yersinia pestis DNA in prairie dog-associated fleas by polymerase chain reaction assay of purified DNA.

J Wildl Dis 2010 Apr;46(2):636-43

Colorado Division of Wildlife, Wildlife Research Center, 317 West Prospect Road, Fort Collins, Colorado 80526-2097, USA.

We evaluated, refined, and applied well-established polymerase chain reaction (PCR) techniques for detecting Yersinia pestis DNA in fleas (mainly Oropsylla spp.) collected from prairie dog (Cynomys spp.) burrows. Based on results from PCR of avirulent Y. pestis strain A1122 DNA, we used DNA purification and primers for the plasminogen activator gene to screen field-collected fleas. We detected Y. pestis DNA in flea pools from two black-tailed prairie dog (Cynomys ludovicianus) colonies with evidence of recent plague epizootics, and from one of four white-tailed prairie dog (Cynomys leucurus) colony complexes (Wolf Creek) where evidence of epizootic plague was lacking. Relative flea abundance and occurrence of Y. pestis DNA among flea pools appeared to vary over time at Wolf Creek. Both DNA purification and primer sequences appeared to influence the likelihood of detecting Y. pestis DNA by PCR in fleas collected from prairie dog burrows in the absence of observed epizootic plague. Presence of Y. pestis plasmid DNA in fleas collected from prairie dog burrows at Wolf Creek may represent evidence that infected fleas were somehow being maintained in that system between epizootics, consistent with the hypothesized enzootic maintenance of plague in prairie dog colony complexes elsewhere.
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http://dx.doi.org/10.7589/0090-3558-46.2.636DOI Listing
April 2010

Effects of selenium supplementation and sample storage time on blood indices of selenium status in bighorn sheep.

J Wildl Dis 2009 Jul;45(3):795-801

Colorado Division of Wildlife, Wildlife Research Center, Fort Collins, CO 80526-2097, USA.

Periodic pneumonia outbreaks cause large-scale die-offs that threaten the viability of bighorn sheep (Ovis canadensis) populations. Bighorns are highly susceptible to pneumonia, and in some cases this susceptibility may be exacerbated by trace mineral deficiencies. To evaluate responses to injectable selenium supplementation, eight captive bighorn sheep were treated with either an injectable sodium selenite supplement or a saline control. We collected 6-ml blood aliquots before and at 1, 6, and 12 wk posttreatment. We submitted one set of aliquots immediately to measure selenium (Se) and zinc (Zn) concentrations and glutathione-peroxidase (GSH-Px) activity; additional aliquots were held at about 22 C and then submitted at 1, 3, and 7 days postcollection to assess effects of storage on these measures. Neither Se nor GSH-Px were affected by selenite injections. Both Se and GSH-Px demonstrated small linear decays over the 7-day storage period (0.011 ppm/day [SE=0.0027] and 15.78 mmole/l/sec/day [SE=6.88], respectively); in contrast, Zn concentrations in stored samples increased logarithmically (0.35 ppm/day on the natural log scale). Blood Se and GSH-Px were not correlated in sampled bighorns; however, because all values for both measures were within normal limits, lack of correlation did not affect interpretation of these data in our study.
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http://dx.doi.org/10.7589/0090-3558-45.3.795DOI Listing
July 2009

Homing endonuclease I-CreI derivatives with novel DNA target specificities.

Nucleic Acids Res 2006 13;34(17):4791-800. Epub 2006 Sep 13.

Department of Biology and Program in Molecular Biology, Pomona College, 175 West 6th Street, Claremont, CA 91711, USA.

Homing endonucleases are highly specific enzymes, capable of recognizing and cleaving unique DNA sequences in complex genomes. Since such DNA cleavage events can result in targeted allele-inactivation and/or allele-replacement in vivo, the ability to engineer homing endonucleases matched to specific DNA sequences of interest would enable powerful and precise genome manipulations. We have taken a step-wise genetic approach in analyzing individual homing endonuclease I-CreI protein/DNA contacts, and describe here novel interactions at four distinct target site positions. Crystal structures of two mutant endonucleases reveal the molecular interactions responsible for their altered DNA target specificities. We also combine novel contacts to create an endonuclease with the predicted target specificity. These studies provide important insights into engineering homing endonucleases with novel target specificities, as well as into the evolution of DNA recognition by this fascinating family of proteins.
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http://dx.doi.org/10.1093/nar/gkl645DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635285PMC
November 2006
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