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Kister I, Curtin R, Piquet AL, Borko T, Pei J, Banbury BL, Bacon TE, Kim A, Tuen M, Velmurugu Y, Nyovanie S, Selva S, Samanovic MI, Mulligan MJ, Patskovsky Y, Priest J, Cabatingan M, Winger RC, Krogsgaard M, Silverman GJ. Longitudinal study of immunity to SARS-CoV2 in ocrelizumab-treated MS patients up to 2 years after COVID-19 vaccination. Ann Clin Transl Neurol 2024. [PMID: 38713096 DOI: 10.1002/acn3.52081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/04/2024] [Accepted: 04/06/2024] [Indexed: 05/08/2024] Open
Abstract
OBJECTIVES (1) To plot the trajectory of humoral and cellular immune responses to the primary (two-dose) COVID-19 mRNA series and the third/booster dose in B-cell-depleted multiple sclerosis (MS) patients up to 2 years post-vaccination; (2) to identify predictors of immune responses to vaccination; and (3) to assess the impact of intercurrent COVID-19 infections on SARS CoV-2-specific immunity. METHODS Sixty ocrelizumab-treated MS patients were enrolled from NYU (New York) and University of Colorado (Anschutz) MS Centers. Samples were collected pre-vaccination, and then 4, 12, 24, and 48 weeks post-primary series, and 4, 12, 24, and 48 weeks post-booster. Binding anti-Spike antibody responses were assessed with multiplex bead-based immunoassay (MBI) and electrochemiluminescence (Elecsys®, Roche Diagnostics), and neutralizing antibody responses with live-virus immunofluorescence-based microneutralization assay. Spike-specific cellular responses were assessed with IFNγ/IL-2 ELISpot (Invitrogen) and, in a subset, by sequencing complementarity determining regions (CDR)-3 within T-cell receptors (Adaptive Biotechnologies). A linear mixed-effect model was used to compare antibody and cytokine levels across time points. Multivariate analyses identified predictors of immune responses. RESULTS The primary vaccination induced an 11- to 208-fold increase in binding and neutralizing antibody levels and a 3- to 4-fold increase in IFNγ/IL-2 responses, followed by a modest decline in antibody but not cytokine responses. Booster dose induced a further 3- to 5-fold increase in binding antibodies and 4- to 5-fold increase in IFNγ/IL-2, which were maintained for up to 1 year. Infections had a variable impact on immunity. INTERPRETATION Humoral and cellular benefits of COVID-19 vaccination in B-cell-depleted MS patients were sustained for up to 2 years when booster doses were administered.
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Affiliation(s)
- Ilya Kister
- NYU Multiple Sclerosis Comprehensive Care Center, Department of Neurology, New York University Grossman School of Medicine, New York, New York, USA
| | - Ryan Curtin
- Laura and Isaac Perlmutter Cancer Center and Department of Pathology, NYU Grossman School of Medicine, New York, New York, USA
| | - Amanda L Piquet
- Rocky Mountain MS Center, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Tyler Borko
- Rocky Mountain MS Center, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Jinglan Pei
- Genentech, Inc., South San Francisco, California, USA
| | | | - Tamar E Bacon
- NYU Multiple Sclerosis Comprehensive Care Center, Department of Neurology, New York University Grossman School of Medicine, New York, New York, USA
| | - Angie Kim
- NYU Multiple Sclerosis Comprehensive Care Center, Department of Neurology, New York University Grossman School of Medicine, New York, New York, USA
| | - Michael Tuen
- NYU Langone Vaccine Center and Department of Medicine, NYU Grossman School of Medicine, New York, New York, USA
| | - Yogambigai Velmurugu
- Laura and Isaac Perlmutter Cancer Center and Department of Pathology, NYU Grossman School of Medicine, New York, New York, USA
| | - Samantha Nyovanie
- Laura and Isaac Perlmutter Cancer Center and Department of Pathology, NYU Grossman School of Medicine, New York, New York, USA
| | - Sean Selva
- Rocky Mountain MS Center, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Marie I Samanovic
- NYU Langone Vaccine Center and Department of Medicine, NYU Grossman School of Medicine, New York, New York, USA
| | - Mark J Mulligan
- NYU Langone Vaccine Center and Department of Medicine, NYU Grossman School of Medicine, New York, New York, USA
| | - Yury Patskovsky
- Laura and Isaac Perlmutter Cancer Center and Department of Pathology, NYU Grossman School of Medicine, New York, New York, USA
| | | | | | - Ryan C Winger
- Genentech, Inc., South San Francisco, California, USA
| | - Michelle Krogsgaard
- Laura and Isaac Perlmutter Cancer Center and Department of Pathology, NYU Grossman School of Medicine, New York, New York, USA
| | - Gregg J Silverman
- Division of Rheumatology, Department of Medicine, NYU Grossman School of Medicine, New York, New York, USA
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Kister I, Curtin R, Pei J, Perdomo K, Bacon TE, Voloshyna I, Kim J, Tardio E, Velmurugu Y, Nyovanie S, Valeria Calderon A, Dibba F, Stanzin I, Samanovic MI, Raut P, Raposo C, Priest J, Cabatingan M, Winger RC, Mulligan MJ, Patskovsky Y, Silverman GJ, Krogsgaard M. Hybrid and vaccine-induced immunity against SAR-CoV-2 in MS patients on different disease-modifying therapies. Ann Clin Transl Neurol 2022; 9:1643-1659. [PMID: 36165097 PMCID: PMC9538694 DOI: 10.1002/acn3.51664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 09/07/2022] [Indexed: 01/12/2023] Open
Abstract
OBJECTIVE To compare "hybrid immunity" (prior COVID-19 infection plus vaccination) and post-vaccination immunity to SARS CoV-2 in MS patients on different disease-modifying therapies (DMTs) and to assess the impact of vaccine product and race/ethnicity on post-vaccination immune responses. METHODS Consecutive MS patients from NYU MS Care Center (New York, NY), aged 18-60, who completed primary COVID-19 vaccination series ≥6 weeks previously were evaluated for SARS CoV-2-specific antibody responses with electro-chemiluminescence and multiepitope bead-based immunoassays and, in a subset, live virus immunofluorescence-based microneutralization assay. SARS CoV-2-specific cellular responses were assessed with cellular stimulation TruCulture IFNγ and IL-2 assay and, in a subset, with IFNγ and IL-2 ELISpot assays. Multivariate analyses examined associations between immunologic responses and prior COVID-19 infection while controlling for age, sex, DMT at vaccination, time-to-vaccine, and vaccine product. RESULTS Between 6/01/2021 and 11/11/2021, 370 MS patients were recruited (mean age 40.6 years; 76% female; 53% non-White; 22% with prior infection; common DMT classes: ocrelizumab 40%; natalizumab 15%, sphingosine-1-phosphate receptor modulators 13%; and no DMT 8%). Vaccine-to-collection time was 18.7 (±7.7) weeks and 95% of patients received mRNA vaccines. In multivariate analyses, patients with laboratory-confirmed prior COVID-19 infection had significantly increased antibody and cellular post-vaccination responses compared to those without prior infection. Vaccine product and DMT class were independent predictors of antibody and cellular responses, while race/ethnicity was not. INTERPRETATION Prior COVID-19 infection is associated with enhanced antibody and cellular post-vaccine responses independent of DMT class and vaccine type. There were no differences in immune responses across race/ethnic groups.
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Affiliation(s)
- Ilya Kister
- NYU Multiple Sclerosis Comprehensive Care Center, Department of NeurologyNew York University Grossman School of MedicineNew YorkNew York10016USA
| | - Ryan Curtin
- Laura and Isaac Perlmutter Cancer Center and Department of PathologyNew York University Grossman School of MedicineNew YorkNew York10016USA
| | - Jinglan Pei
- Genentech, Inc.South San FranciscoCaliforniaUSA
| | - Katherine Perdomo
- NYU Multiple Sclerosis Comprehensive Care Center, Department of NeurologyNew York University Grossman School of MedicineNew YorkNew York10016USA
| | - Tamar E. Bacon
- NYU Multiple Sclerosis Comprehensive Care Center, Department of NeurologyNew York University Grossman School of MedicineNew YorkNew York10016USA
| | - Iryna Voloshyna
- Laura and Isaac Perlmutter Cancer Center and Department of PathologyNew York University Grossman School of MedicineNew YorkNew York10016USA
| | - Joseph Kim
- Laura and Isaac Perlmutter Cancer Center and Department of PathologyNew York University Grossman School of MedicineNew YorkNew York10016USA
| | - Ethan Tardio
- Laura and Isaac Perlmutter Cancer Center and Department of PathologyNew York University Grossman School of MedicineNew YorkNew York10016USA
| | - Yogambigai Velmurugu
- Laura and Isaac Perlmutter Cancer Center and Department of PathologyNew York University Grossman School of MedicineNew YorkNew York10016USA
| | - Samantha Nyovanie
- Laura and Isaac Perlmutter Cancer Center and Department of PathologyNew York University Grossman School of MedicineNew YorkNew York10016USA
| | - Andrea Valeria Calderon
- Laura and Isaac Perlmutter Cancer Center and Department of PathologyNew York University Grossman School of MedicineNew YorkNew York10016USA
| | - Fatoumatta Dibba
- Laura and Isaac Perlmutter Cancer Center and Department of PathologyNew York University Grossman School of MedicineNew YorkNew York10016USA
| | - Igda Stanzin
- Laura and Isaac Perlmutter Cancer Center and Department of PathologyNew York University Grossman School of MedicineNew YorkNew York10016USA
| | - Marie I. Samanovic
- NYU Langone Vaccine Center, Department of MedicineNYU Grossman School of MedicineNew YorkNew YorkUSA
| | - Pranil Raut
- Genentech, Inc.South San FranciscoCaliforniaUSA
| | | | | | | | | | - Mark J. Mulligan
- NYU Langone Vaccine Center, Department of MedicineNYU Grossman School of MedicineNew YorkNew YorkUSA
| | - Yury Patskovsky
- Laura and Isaac Perlmutter Cancer Center and Department of PathologyNew York University Grossman School of MedicineNew YorkNew York10016USA
| | - Gregg J. Silverman
- Division of Rheumatology, Department of MedicineNew York University Grossman School of MedicineNew YorkNew York10016USA
| | - Michelle Krogsgaard
- Laura and Isaac Perlmutter Cancer Center and Department of PathologyNew York University Grossman School of MedicineNew YorkNew York10016USA
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Kister I, Patskovsky Y, Curtin R, Pei J, Perdomo K, Rimler Z, Voloshyna I, Samanovic MI, Cornelius AR, Velmurugu Y, Nyovanie S, Kim J, Tardio E, Bacon TE, Zhovtis Ryerson L, Raut P, Rosetta P, Hawker K, Raposo C, Priest J, Cabatingan M, Winger RC, Mulligan MJ, Krogsgaard M, Silverman GJ. Cellular and humoral immunity to SARS-CoV-2 infection in multiple sclerosis patients on ocrelizumab and other disease-modifying therapies: a multi-ethnic observational study. Ann Neurol 2022; 91:782-795. [PMID: 35289960 PMCID: PMC9082484 DOI: 10.1002/ana.26346] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 11/12/2022]
Abstract
OBJECTIVE To determine the impact of MS disease-modifying therapies (DMTs) on the development of cellular and humoral immunity to SARS-CoV-2 infection. METHODS MS patients aged 18-60 were evaluated for anti-nucleocapsid and anti-Spike RBD antibody with electro-chemiluminescence immunoassay; antibody responses to Spike protein, RBD, N-terminal domain with multiepitope bead-based immunoassays (MBI); live virus immunofluorescence-based microneutralization assay; T-cell responses to SARS-CoV-2 Spike using TruCulture ELISA; and IL-2 and IFNγ ELISpot assays. Assay results were compared by DMT class. Spearman correlation and multivariate analyses were performed to examine associations between immunologic responses and infection severity. RESULTS Between 1/6/2021 and 7/21/2021, 389 MS patients were recruited (mean age 40.3 years; 74% female; 62% non-White). Most common DMTs were ocrelizumab (OCR) - 40%; natalizumab - 17%, Sphingosine 1-phosphate receptor (S1P) modulators -12%; and 15% untreated. 177 patients (46%) had laboratory evidence of SARS-CoV-2 infection; 130 had symptomatic infection, 47 - asymptomatic. Antibody responses were markedly attenuated in OCR compared to other groups (p≤0.0001). T-cell responses (IFNγ) were decreased in S1P (p=0.03), increased in natalizumab (p<0.001), and similar in other DMTs, including OCR. Cellular and humoral responses were moderately correlated in both OCR (r=0.45, p=0.0002) and non-OCR (r=0.64, p<0.0001). Immune responses did not differ by race/ethnicity. COVID-19 clinical course was mostly non-severe and similar across DMTs; 7% (9/130) were hospitalized. INTERPRETATION DMTs had differential effects on humoral and cellular immune responses to SARS-CoV-2 infection. Immune responses did not correlate with COVID-19 clinical severity in this relatively young and non-disabled group of MS patients. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Ilya Kister
- NYU Multiple Sclerosis Comprehensive Care Center, Department of Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Yury Patskovsky
- Laura and Isaac Perlmutter Cancer Center and Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Ryan Curtin
- Laura and Isaac Perlmutter Cancer Center and Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Jinglan Pei
- Genentech, Inc., South San Francisco, CA, USA
| | - Katherine Perdomo
- NYU Multiple Sclerosis Comprehensive Care Center, Department of Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Zoe Rimler
- NYU Multiple Sclerosis Comprehensive Care Center, Department of Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Iryna Voloshyna
- Laura and Isaac Perlmutter Cancer Center and Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Marie I Samanovic
- NYU Langone Vaccine Center, Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Amber R Cornelius
- NYU Langone Vaccine Center, Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Yogambigai Velmurugu
- Laura and Isaac Perlmutter Cancer Center and Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Samantha Nyovanie
- Laura and Isaac Perlmutter Cancer Center and Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Joseph Kim
- Laura and Isaac Perlmutter Cancer Center and Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Ethan Tardio
- Laura and Isaac Perlmutter Cancer Center and Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Tamar E Bacon
- NYU Multiple Sclerosis Comprehensive Care Center, Department of Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Lana Zhovtis Ryerson
- NYU Multiple Sclerosis Comprehensive Care Center, Department of Neurology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Pranil Raut
- Genentech, Inc., South San Francisco, CA, USA
| | | | | | | | | | | | | | - Mark J Mulligan
- NYU Langone Vaccine Center, Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Michelle Krogsgaard
- Laura and Isaac Perlmutter Cancer Center and Department of Pathology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Gregg J Silverman
- Division of Rheumatology, Department of Medicine, New York University Grossman School of Medicine, New York, NY, 10016, USA
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Krogsgaard M, Natarajan A, Velmurugu Y, Yuan Z, Ge C, Nadarajah V, Cardozo T, Bracken WC, Zhu C. Modulating extracellular TCR-CD3 interaction to identify new immunotherapy targets against cancer. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.239.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
T cell recognition of antigen and resulting proximal signaling are key steps in the initiation of the adaptive immune response. Previous studies targeting antigen binding site for enhancing T-cell responses to tumor antigens often lead to off-target effects and toxicity. Recently, we used nuclear magnetic resonance (NMR) spectroscopy, mutational analysis and computational docking to derive a 3D structure of the extracellular TCR-CD3 assembly. Further, biomolecular force probe (BFP) measurements allowed us to determine how 2D affinity and force-modulated TCR-pMHC kinetics depend on TCR-CD3 interaction sites and affect transduction of extracellular pMHC-TCR ligation into T cell function. Based on our TCR-CD3 structural model and binding data, we generated TCR libraries for a melanoma-specific TCR (DMF5) using site-specific mutagenesis in the Cbhelix 3 and helix 4-F strand regions of the TCR to optimize the TCR-CD3 interaction and to select for mutants with enhanced T-cell effector function. One Cb helix 4-F strand mutant, NP202203AA showed increased T cell response to antigen and showed enhanced TCR-pMHC bond lifetime (catch-bonds) in BFP assays leading to prolonged T cell signaling. In the future, DMF5 TCR with reengineered CD3 binding regions will be used in tumor rejection in pre-clinical mouse melanoma models for efficacy and toxicity to develop more effective T cell therapies for human targets.
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Velmurugu Y, Vivas P, Connolly M, Kuznetsov SV, Rice PA, Ansari A. Two-step interrogation then recognition of DNA binding site by Integration Host Factor: an architectural DNA-bending protein. Nucleic Acids Res 2019; 46:1741-1755. [PMID: 29267885 PMCID: PMC5829579 DOI: 10.1093/nar/gkx1215] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 12/08/2017] [Indexed: 12/23/2022] Open
Abstract
The dynamics and mechanism of how site-specific DNA-bending proteins initially interrogate potential binding sites prior to recognition have remained elusive for most systems. Here we present these dynamics for Integration Host factor (IHF), a nucleoid-associated architectural protein, using a μs-resolved T-jump approach. Our studies show two distinct DNA-bending steps during site recognition by IHF. While the faster (∼100 μs) step is unaffected by changes in DNA or protein sequence that alter affinity by >100-fold, the slower (1–10 ms) step is accelerated ∼5-fold when mismatches are introduced at DNA sites that are sharply kinked in the specific complex. The amplitudes of the fast phase increase when the specific complex is destabilized and decrease with increasing [salt], which increases specificity. Taken together, these results indicate that the fast phase is non-specific DNA bending while the slow phase, which responds only to changes in DNA flexibility at the kink sites, is specific DNA kinking during site recognition. Notably, the timescales for the fast phase overlap with one-dimensional diffusion times measured for several proteins on DNA, suggesting that these dynamics reflect partial DNA bending during interrogation of potential binding sites by IHF as it scans DNA.
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Affiliation(s)
- Yogambigai Velmurugu
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Paula Vivas
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Mitchell Connolly
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Serguei V Kuznetsov
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Phoebe A Rice
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Anjum Ansari
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA.,Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA
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Chen X, Velmurugu Y, Zheng G, Park B, Shim Y, Kim Y, Liu L, Van Houten B, He C, Ansari A, Min JH. Kinetic gating mechanism of DNA damage recognition by Rad4/XPC. Nat Commun 2015; 6:5849. [PMID: 25562780 PMCID: PMC4354021 DOI: 10.1038/ncomms6849] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 11/13/2014] [Indexed: 01/24/2023] Open
Abstract
The xeroderma pigmentosum C (XPC) complex initiates nucleotide excision repair by recognizing DNA lesions before recruiting downstream factors. How XPC detects structurally diverse lesions embedded within normal DNA is unknown. Here we present a crystal structure that captures the yeast XPC orthologue (Rad4) on a single register of undamaged DNA. The structure shows that a disulphide-tethered Rad4 flips out normal nucleotides and adopts a conformation similar to that seen with damaged DNA. Contrary to many DNA repair enzymes that can directly reject non-target sites as structural misfits, our results suggest that Rad4/XPC uses a kinetic gating mechanism whereby lesion selectivity arises from the kinetic competition between DNA opening and the residence time of Rad4/XPC per site. This mechanism is further supported by measurements of Rad4-induced lesion-opening times using temperature-jump perturbation spectroscopy. Kinetic gating may be a general mechanism used by site-specific DNA-binding proteins to minimize time-consuming interrogations of non-target sites. XPC nucleotide excision repair factor is key to starting the repair of diverse helix-distorting DNA lesions caused by environmental insults. Here, the authors propose a kinetic gating mechanism whereby XPC recognizes DNA lesions by preferentially opening damaged sites while readily diffusing away from undamaged sites.
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Affiliation(s)
- Xuejing Chen
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607, USA
| | - Yogambigai Velmurugu
- Department of Physics, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607, USA
| | - Guanqun Zheng
- Department of Chemistry, Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th Street, Chicago, Illinois 60637, USA
| | - Beomseok Park
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607, USA
| | - Yoonjung Shim
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607, USA
| | - Youngchang Kim
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, Illinois 60439, USA
| | - Lili Liu
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine and University of Pittsburgh Cancer Institute, University of Pittsburgh, 5117 Centre Avenue, Pittsburgh, Pennsylvania 15213, USA
| | - Bennett Van Houten
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine and University of Pittsburgh Cancer Institute, University of Pittsburgh, 5117 Centre Avenue, Pittsburgh, Pennsylvania 15213, USA
| | - Chuan He
- Department of Chemistry, Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th Street, Chicago, Illinois 60637, USA
| | - Anjum Ansari
- 1] Department of Physics, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607, USA [2] Department of Bioengineering, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607, USA
| | - Jung-Hyun Min
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607, USA
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Roca J, Velmurugu Y, Narayanan R, Narayanan P, Kouznetsov S, Ansari A. RNA Pseudoknot Folding Energy Landscape Elucidated with T-Jump Measurements and Kinetic Modeling. Biophys J 2015. [DOI: 10.1016/j.bpj.2014.11.1307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Vivas P, Velmurugu Y, Kuznetsov SV, Rice PA, Ansari A. Global analysis of ion dependence unveils hidden steps in DNA binding and bending by integration host factor. J Chem Phys 2014; 139:121927. [PMID: 24089739 DOI: 10.1063/1.4818596] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Proteins that recognize and bind to specific sites on DNA often distort the DNA at these sites. The rates at which these DNA distortions occur are considered to be important in the ability of these proteins to discriminate between specific and nonspecific sites. These rates have proven difficult to measure for most protein-DNA complexes in part because of the difficulty in separating the kinetics of unimolecular conformational rearrangements (DNA bending and kinking) from the kinetics of bimolecular complex association and dissociation. A notable exception is the Integration Host Factor (IHF), a eubacterial architectural protein involved in chromosomal compaction and DNA recombination, which binds with subnanomolar affinity to specific DNA sites and bends them into sharp U-turns. The unimolecular DNA bending kinetics has been resolved using both stopped-flow and laser temperature-jump perturbation. Here we expand our investigation by presenting a global analysis of the ionic strength dependence of specific binding affinity and relaxation kinetics of an IHF-DNA complex. This analysis enables us to obtain each of the underlying elementary rates (DNA bending/unbending and protein-DNA association/dissociation), and their ionic strength dependence, even under conditions where the two processes are coupled. Our analysis indicates interesting differences in the ionic strength dependence of the bi- versus unimolecular steps. At moderate [KCl] (100-500 mM), nearly all the ionic strength dependence to the overall equilibrium binding affinity appears in the bimolecular association/dissociation of an initial, presumably weakly bent, encounter complex, with a slope SK(bi) ≈ 8 describing the loglog-dependence of the equilibrium constant to form this complex on [KCl]. In contrast, the unimolecular equilibrium constant to form the fully wrapped specific complex from the initial complex is nearly independent of [KCl], with SK(uni) < 0.5. This result is counterintuitive because there are at least twice as many ionic protein-DNA contacts in the fully wrapped complex than in the weakly bent intermediate. The following picture emerges from this analysis: in the bimolecular step, the observed [KCl]-dependence is consistent with the number of DNA counterions expected to be released when IHF binds nonspecifically to DNA whereas in the unimolecular reorganization step, the weak [KCl]-dependence suggests that two effects cancel one another. On one hand, formation of additional protein-DNA contacts in the fully wrapped complex releases bound counterions into bulk solution, which is entropically favored by decreasing [salt]. On the other hand, formation of the fully wrapped complex also releases tightly bound water molecules, which is osmotically favored by increasing [salt]. More generally, our global analysis strategy is applicable to other protein-DNA complexes, and opens up the possibility of measuring DNA bending rates in complexes where the unimolecular and bimolecular steps are not easily separable.
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Affiliation(s)
- Paula Vivas
- Department of Physics, University of Illinois at Chicago, Chicago, Illinois 60607, USA
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Narayanan R, Zhu L, Velmurugu Y, Roca J, Kuznetsov SV, Prehna G, Lapidus LJ, Ansari A. Exploring the Energy Landscape of Nucleic Acid Hairpins Using Laser Temperature-Jump and Microfluidic Mixing. J Am Chem Soc 2012; 134:18952-63. [DOI: 10.1021/ja301218e] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
| | - Li Zhu
- Department of Physics
and Astronomy, Michigan State University, East Lansing, Michigan 48824,
United States
- Advanced
Photonics Center, Southeast University,
Nanjing 210096, China
| | | | | | | | | | - Lisa J. Lapidus
- Department of Physics
and Astronomy, Michigan State University, East Lansing, Michigan 48824,
United States
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10
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Abstract
RNA pseudoknots are examples of minimal structural motifs in RNA with tertiary interactions that stabilize the structures of many ribozymes. They also play an essential role in a variety of biological functions that are modulated by their structure, stability, and dynamics. Therefore, understanding the global principles that determine the thermodynamics and folding pathways of RNA pseudoknots is an important problem in biology, both for elucidating the folding mechanisms of larger ribozymes as well as addressing issues of possible kinetic control of the biological functions of pseudoknots. We report on the folding/unfolding kinetics of a hairpin-type pseudoknot obtained with microsecond time-resolution in response to a laser temperature-jump perturbation. The kinetics are monitored using UV absorbance as well as fluorescence of extrinsically attached labels as spectroscopic probes of the transiently populated RNA conformations. We measure folding times of 1-6 ms at 37 °C, which are at least 100-fold faster than previous observations of very slow folding pseudoknots that were trapped in misfolded conformations. The measured relaxation times are remarkably similar to predictions of a computational study by Thirumalai and co-workers (Cho, S. S.; Pincus, D.L.; Thirumalai, D. Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 17349-17354). Thus, these studies provide the first observation of a fast-folding pseudoknot and present a benchmark against which computational models can be refined.
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Affiliation(s)
- Ranjani Narayanan
- Department of Physics (M/C 273), University of Illinois at Chicago, 845 W. Taylor St., Chicago, Illinois 60607, USA
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West K, Bay L, Nielsen MM, Velmurugu Y, Skaarup S. Electronic Conductivity of Polypyrrole−Dodecyl Benzene Sulfonate Complexes. J Phys Chem B 2004. [DOI: 10.1021/jp048153m] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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