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Article ; Online: Relaxation and single site multiple mutations to identify and control allosteric networks.

Lee, Eunjeong / Redzic, Jasmina S / Zohar Eisenmesser, Elan

2023 Volume 216, Page(s) 51–57

Abstract: Advances in Nuclear Magnetic Resonance (NMR) spectroscopy have allowed for the identification and characterization of movements in enzymes over the last 20 years that has also revealed the complexities of allosteric coupling. For example, many of the ... ...

Abstract	Advances in Nuclear Magnetic Resonance (NMR) spectroscopy have allowed for the identification and characterization of movements in enzymes over the last 20 years that has also revealed the complexities of allosteric coupling. For example, many of the inherent movements of enzymes, and proteins in general, have been shown to be highly localized but nonetheless still coupled over long distances. Such partial couplings provide challenges to both identifying allosteric networks of dynamic communication and determining their roles in catalytic function. We have developed an approach to help identify and engineer enzyme function, called Relaxation And Single Site Multiple Mutations (RASSMM). This approach is a powerful extension of mutagenesis and NMR that is based on the observation that multiple mutations to a single site distal to the active site allosterically induces different effects to networks. Such an approach generates a panel of mutations that can also be subjected to functional studies in order to match catalytic effects with changes to coupled networks. In this review, the RASSMM approach is briefly outlined together with two applications that include cyclophilin-A and Biliverdin Reductase B.
MeSH term(s)	Mutation ; Proteins/chemistry ; Mutagenesis ; Magnetic Resonance Spectroscopy ; Catalytic Domain ; Allosteric Regulation
Chemical Substances	Proteins
Language	English
Publishing date	2023-06-09
Publishing country	United States
Document type	Review ; Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1066584-5
ISSN	1095-9130 ; 1046-2023
ISSN (online)	1095-9130
ISSN	1046-2023
DOI	10.1016/j.ymeth.2023.06.002
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Article: Identifying structural and dynamic changes during the Biliverdin Reductase B catalytic cycle.

Lee, Eunjeong / McLeod, Matthew J / Redzic, Jasmina S / Marcolin, Barbara / Thorne, Robert E / Agarwal, Pratul / Eisenmesser, Elan Zohar

Frontiers in molecular biosciences

2023 Volume 10, Page(s) 1244587

Abstract: Biliverdin Reductase B (BLVRB) is an NADPH-dependent reductase that catalyzes the reduction of multiple substrates and is therefore considered a critical cellular redox regulator. In this study, we sought to address whether both structural and dynamics ... ...

Abstract	Biliverdin Reductase B (BLVRB) is an NADPH-dependent reductase that catalyzes the reduction of multiple substrates and is therefore considered a critical cellular redox regulator. In this study, we sought to address whether both structural and dynamics changes occur between different intermediates of the catalytic cycle and whether these were relegated to just the active site or the entirety of the enzyme. Through X-ray crystallography, we determined the apo BLVRB structure for the first time, revealing subtle global changes compared to the holo structure and identifying the loss of a critical hydrogen bond that "clamps" the R78-loop over the coenzyme. Amide and Cα chemical shift perturbations were used to identify environmental and secondary structural changes between intermediates, with more distant global changes observed upon coenzyme binding compared to substrate interactions. NMR relaxation rate measurements provided insights into the dynamic behavior of BLVRB during the catalytic cycle. Specifically, the inherently dynamic R78-loop that becomes ordered upon coenzyme binding persists through the catalytic cycle while similar regions experience dynamic exchange. However, the dynamic exchange processes were found to differ through the catalytic cycle with several groups of residues exhibiting similar dynamic responses. Finally, both local and distal structural and dynamic changes occur within BLVRB that are dependent solely on the oxidative state of the coenzyme. Thus, through a comprehensive analysis here, this study revealed structural and dynamic alterations in BLVRB through its catalytic cycle that are not simply relegated to the active site, but instead, are allosterically coupled throughout the enzyme.
Language	English
Publishing date	2023-08-14
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2814330-9
ISSN	2296-889X
ISSN	2296-889X
DOI	10.3389/fmolb.2023.1244587
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Article ; Online: Heme sequestration by hemophilin from

Fulte, Sam / Atto, Brianna / McCarty, Arianna / Horn, Kadi J / Redzic, Jasmina S / Eisenmesser, Elan / Yang, Michael / Marsh, Robyn L / Tristram, Stephen / Clark, Sarah E

mSphere

2024 Volume 9, Issue 3, Page(s) e0000624

Abstract: Iron acquisition is a key feature dictating the success of pathogen colonization and infection. Pathogens scavenging iron from the host must contend with other members of the microbiome similarly competing for the limited pool of bioavailable iron, often ...

Abstract	Iron acquisition is a key feature dictating the success of pathogen colonization and infection. Pathogens scavenging iron from the host must contend with other members of the microbiome similarly competing for the limited pool of bioavailable iron, often in the form of heme. In this study, we identify a beneficial role for the heme-binding protein hemophilin (Hpl) produced by the non-pathogenic bacterium Importance: The microbiome provides a critical layer of protection against infection with bacterial pathogens. This protection is accomplished through a variety of mechanisms, including interference with pathogen growth and adherence to host cells. In terms of immune defense, another way to prevent pathogens from establishing infections is by limiting the availability of nutrients, referred to as nutritional immunity. Restricting pathogen access to iron is a central component of this approach. Here, we uncovered an example where these two strategies intersect to impede infection with the respiratory tract bacterial pathogen
MeSH term(s)	Humans ; Haemophilus influenzae ; Heme/metabolism ; Haemophilus Infections ; Lung/microbiology ; Iron ; Haemophilus
Chemical Substances	Heme (42VZT0U6YR) ; Iron (E1UOL152H7)
Language	English
Publishing date	2024-02-21
Publishing country	United States
Document type	Journal Article
ISSN	2379-5042
ISSN (online)	2379-5042
DOI	10.1128/msphere.00006-24
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Article: Modulating Enzyme Function

Redzic, Jasmina S / Duff, Michael R / Blue, Ashley / Pitts, Todd M / Agarwal, Pratul / Eisenmesser, Elan Zohar

Frontiers in molecular biosciences

2021 Volume 8, Page(s) 691208

Abstract: The biliverdin reductase B (BLVRB) class of enzymes catalyze the NADPH-dependent reduction of multiple flavin substrates and are emerging as critical players in cellular redox regulation. However, the role of dynamics and allostery have not been ... ...

Abstract	The biliverdin reductase B (BLVRB) class of enzymes catalyze the NADPH-dependent reduction of multiple flavin substrates and are emerging as critical players in cellular redox regulation. However, the role of dynamics and allostery have not been addressed, prompting studies here that have revealed a position 15 Å away from the active site within human BLVRB (T164) that is inherently dynamic and can be mutated to control global micro-millisecond motions and function. By comparing the inherent dynamics through nuclear magnetic resonance (NMR) relaxation approaches of evolutionarily distinct BLVRB homologues and by applying our previously developed Relaxation And Single Site Multiple Mutations (RASSMM) approach that monitors both the functional and dynamic effects of multiple mutations to the single T164 site, we have discovered that the most dramatic mutagenic effects coincide with evolutionary changes and these modulate coenzyme binding. Thus, evolutionarily changing sites distal to the active site serve as dynamic "dials" to globally modulate motions and function. Despite the distal dynamic and functional coupling modulated by this site, micro-millisecond motions span an order of magnitude in their apparent kinetic rates of motions. Thus, global dynamics within BLVRB are a collection of partially coupled motions tied to catalytic function.
Language	English
Publishing date	2021-05-20
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2814330-9
ISSN	2296-889X
ISSN	2296-889X
DOI	10.3389/fmolb.2021.691208
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Article: Activation Loop Dynamics Are Coupled to Core Motions in Extracellular Signal-Regulated Kinase-2

Iverson, Dylan B / Xiao, Yao / Jones, David N / Eisenmesser, Elan Z / Ahn, Natalie G

Biochemistry. 2020 July 09, v. 59, no. 29

2020

Abstract: The activation loop segment in protein kinases is a common site for regulatory phosphorylation. In extracellular signal-regulated kinase 2 (ERK2), dual phosphorylation and conformational rearrangement of the activation loop accompany enzyme activation. X- ...

Abstract	The activation loop segment in protein kinases is a common site for regulatory phosphorylation. In extracellular signal-regulated kinase 2 (ERK2), dual phosphorylation and conformational rearrangement of the activation loop accompany enzyme activation. X-ray structures show the active conformation to be stabilized by multiple ion pair interactions between phosphorylated threonine and tyrosine residues in the loop and six arginine residues in the kinase core. Despite the extensive salt bridge network, nuclear magnetic resonance Carr–Purcell–Meiboom–Gill relaxation dispersion experiments show that the phosphorylated activation loop is conformationally mobile on a microsecond to millisecond time scale. The dynamics of the loop match those of previously reported global exchange within the kinase core region and surrounding the catalytic site that have been found to facilitate productive nucleotide binding. Mutations in the core region that alter these global motions also alter the dynamics of the activation loop. Conversely, mutations in the activation loop perturb the global exchange within the kinase core. Together, these findings provide evidence for coupling between motions in the activation loop and those surrounding the catalytic site in the active state of the kinase. Thus, the activation loop segment in dual-phosphorylated ERK2 is not held statically in the active X-ray conformation but instead undergoes exchange between conformers separated by a small energetic barrier, serving as part of a dynamic allosteric network controlling nucleotide binding and catalytic function.
Keywords	X-radiation ; active sites ; arginine ; dynamics ; enzyme activation ; mitogen-activated protein kinase ; mutation ; nuclear magnetic resonance spectroscopy ; phosphorylation ; threonine ; tyrosine
Language	English
Dates of publication	2020-0709
Size	p. 2698-2706.
Publishing place	American Chemical Society
Document type	Article
Note	NAL-light
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/acs.biochem.0c00485
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: A substrate-induced gating mechanism is conserved among Gram-positive IgA1 metalloproteases.

Redzic, Jasmina S / Rahkola, Jeremy / Tran, Norman / Holyoak, Todd / Lee, Eunjeong / Martín-Galiano, Antonio Javier / Meyer, Nancy / Zheng, Hongjin / Eisenmesser, Elan

Communications biology

2022 Volume 5, Issue 1, Page(s) 1190

Abstract: The mucosal adaptive immune response is dependent on the production of IgA antibodies and particularly IgA1, yet opportunistic bacteria have evolved mechanisms to specifically block this response by producing IgA1 proteases (IgA1Ps). Our lab was the ... ...

Abstract	The mucosal adaptive immune response is dependent on the production of IgA antibodies and particularly IgA1, yet opportunistic bacteria have evolved mechanisms to specifically block this response by producing IgA1 proteases (IgA1Ps). Our lab was the first to describe the structures of a metal-dependent IgA1P (metallo-IgA1P) produced from Gram-positive Streptococcus pneumoniae both in the absence and presence of its IgA1 substrate through cryo-EM single particle reconstructions. This prior study revealed an active-site gating mechanism reliant on substrate-induced conformational changes to the enzyme that begged the question of whether such a mechanism is conserved among the wider Gram-positive metallo-IgA1P subfamily of virulence factors. Here, we used cryo-EM to characterize the metallo-IgA1P of a more distantly related family member from Gemella haemolysans, an emerging opportunistic pathogen implicated in meningitis, endocarditis, and more recently bacteremia in the elderly. While the substrate-free structures of these two metallo-IgA1Ps exhibit differences in the relative starting positions of the domain responsible for gating substrate, the enzymes have similar domain orientations when bound to IgA1. Together with biochemical studies that indicate these metallo-IgA1Ps have similar binding affinities and activities, these data indicate that metallo-IgA1P binding requires the specific IgA1 substrate to open the enzymes for access to their active site and thus, largely conform to an "induced fit" model.
MeSH term(s)	Humans ; Aged ; Immunoglobulin A/metabolism ; Metalloproteases ; Streptococcus/metabolism ; Bacteria/metabolism ; Virulence Factors
Chemical Substances	Immunoglobulin A ; Metalloproteases (EC 3.4.-) ; Virulence Factors
Language	English
Publishing date	2022-11-07
Publishing country	England
Document type	Journal Article
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-022-04173-3
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Article ; Online: Activation Loop Dynamics Are Coupled to Core Motions in Extracellular Signal-Regulated Kinase-2.

Iverson, Dylan B / Xiao, Yao / Jones, David N / Eisenmesser, Elan Z / Ahn, Natalie G

Biochemistry

2020 Volume 59, Issue 29, Page(s) 2698–2706

Abstract	The activation loop segment in protein kinases is a common site for regulatory phosphorylation. In extracellular signal-regulated kinase 2 (ERK2), dual phosphorylation and conformational rearrangement of the activation loop accompany enzyme activation. X-ray structures show the active conformation to be stabilized by multiple ion pair interactions between phosphorylated threonine and tyrosine residues in the loop and six arginine residues in the kinase core. Despite the extensive salt bridge network, nuclear magnetic resonance Carr-Purcell-Meiboom-Gill relaxation dispersion experiments show that the phosphorylated activation loop is conformationally mobile on a microsecond to millisecond time scale. The dynamics of the loop match those of previously reported global exchange within the kinase core region and surrounding the catalytic site that have been found to facilitate productive nucleotide binding. Mutations in the core region that alter these global motions also alter the dynamics of the activation loop. Conversely, mutations in the activation loop perturb the global exchange within the kinase core. Together, these findings provide evidence for coupling between motions in the activation loop and those surrounding the catalytic site in the active state of the kinase. Thus, the activation loop segment in dual-phosphorylated ERK2 is not held statically in the active X-ray conformation but instead undergoes exchange between conformers separated by a small energetic barrier, serving as part of a dynamic allosteric network controlling nucleotide binding and catalytic function.
MeSH term(s)	Animals ; Crystallography, X-Ray ; Enzyme Activation ; Mitogen-Activated Protein Kinase 1/chemistry ; Models, Molecular ; Motion ; Nuclear Magnetic Resonance, Biomolecular ; Phosphorylation ; Protein Conformation ; Rats
Chemical Substances	Mapk1 protein, rat (EC 2.7.11.24) ; Mitogen-Activated Protein Kinase 1 (EC 2.7.11.24)
Language	English
Publishing date	2020-07-15
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/acs.biochem.0c00485
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Article ; Online: Molecular insight into the specific interactions of the SARS-Coronavirus-2 nucleocapsid with RNA and host protein.

Lee, Eunjeong / Redzic, Jasmina S / Saviola, Anthony J / Li, Xueni / Ebmeier, Christopher C / Kutateladze, Tatiana / Hansen, Kirk Charles / Zhao, Rui / Ahn, Natalie / Sluchanko, Nikolai N / Eisenmesser, Elan

Protein science : a publication of the Protein Society

2023 Volume 32, Issue 4, Page(s) e4603

Abstract: The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) nucleocapsid protein is the most abundantly expressed viral protein during infection where it targets both RNA and host proteins. However, identifying how a single viral protein interacts ... ...

Abstract	The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) nucleocapsid protein is the most abundantly expressed viral protein during infection where it targets both RNA and host proteins. However, identifying how a single viral protein interacts with so many different targets remains a challenge, providing the impetus here for identifying the interaction sites through multiple methods. Through a combination of nuclear magnetic resonance (NMR), electron microscopy, and biochemical methods, we have characterized nucleocapsid interactions with RNA and with three host proteins, which include human cyclophilin-A, Pin1, and 14-3-3τ. Regarding RNA interactions, the nucleocapsid protein N-terminal folded domain preferentially interacts with smaller RNA fragments relative to the C-terminal region, suggesting an initial RNA engagement is largely dictated by this N-terminal region followed by weaker interactions to the C-terminal region. The nucleocapsid protein forms 10 nm ribonuclear complexes with larger RNA fragments that include 200 and 354 nucleic acids, revealing its potential diversity in sequestering different viral genomic regions during viral packaging. Regarding host protein interactions, while the nucleocapsid targets all three host proteins through its serine-arginine-rich region, unstructured termini of the nucleocapsid protein also engage host cyclophilin-A and host 14-3-3τ. Considering these host proteins play roles in innate immunity, the SARS-CoV-2 nucleocapsid protein may block the host response by competing interactions. Finally, phosphorylation of the nucleocapsid protein quenches an inherent dynamic exchange process within its serine-arginine-rich region. Our studies identify many of the diverse interactions that may be important for SARS-CoV-2 pathology during infection.
MeSH term(s)	Humans ; RNA ; SARS-CoV-2/metabolism ; Cyclophilins/analysis ; COVID-19 ; Nucleocapsid/chemistry ; Nucleocapsid/metabolism ; Nucleocapsid Proteins/chemistry ; Nucleocapsid Proteins/genetics ; Nucleocapsid Proteins/metabolism ; Arginine ; Serine ; NIMA-Interacting Peptidylprolyl Isomerase/analysis
Chemical Substances	RNA (63231-63-0) ; Cyclophilins (EC 5.2.1.-) ; Nucleocapsid Proteins ; Arginine (94ZLA3W45F) ; Serine (452VLY9402) ; PIN1 protein, human (EC 5.2.1.8) ; NIMA-Interacting Peptidylprolyl Isomerase
Language	English
Publishing date	2023-02-20
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1106283-6
ISSN	1469-896X ; 0961-8368
ISSN (online)	1469-896X
ISSN	0961-8368
DOI	10.1002/pro.4603
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Zs.A 3407: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: International nomenclature guidelines for the IL-1 family of cytokines and receptors.

Nature immunology

2024 Volume 25, Issue 4, Page(s) 581–582

MeSH term(s)	Cytokines ; Interleukin-1
Chemical Substances	Cytokines ; Interleukin-1
Language	English
Publishing date	2024-03-18
Publishing country	United States
Document type	Letter
ZDB-ID	2016987-5
ISSN	1529-2916 ; 1529-2908
ISSN (online)	1529-2916
ISSN	1529-2908
DOI	10.1038/s41590-024-01777-1
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Zs.A 5294: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Protect, repair, destroy or sacrifice: a role of oxidative stress biology in inter-donor variability of blood storage?

D'Alessandro, Angelo / Hansen, Kirk C / Eisenmesser, Elan Z / Zimring, James C

Blood transfusion = Trasfusione del sangue

2019 Volume 17, Issue 4, Page(s) 281–288

Abstract: Red blood cells (RBCs) have been historically regarded as a critical model to investigate cellular and oxidant stress biology. First of all, they are constantly exposed to oxidant stress, as their main function is to transport and deliver oxygen to ... ...

Abstract	Red blood cells (RBCs) have been historically regarded as a critical model to investigate cellular and oxidant stress biology. First of all, they are constantly exposed to oxidant stress, as their main function is to transport and deliver oxygen to tissues. Second, they are devoid of de novo protein synthesis capacity, which prevents RBCs from replacing irreversibly oxidised proteins with newly synthesised ones. As such, RBCs have evolved to (i) protect themselves from oxidant stress, in order to prevent oxidant damage from reactive species; (ii) repair oxidatively damaged proteins, through mechanisms that involve glutathione and one-carbon metabolism; (iii) destroy irreversibly oxidised proteins through proteasomal or protease-dependent degradation; and (iv) sacrifice membrane portions through mechanism of vesiculation. In this brief review we will summarize these processes and their relevance to RBC redox biology (within the context of blood storage), with a focus on how polymorphisms in RBC antioxidant responses could contribute to explaining the heterogeneity in the progression and severity of the RBC storage lesion that can be observed across the healthy donor population.
MeSH term(s)	Animals ; Blood Donors ; Blood Preservation/methods ; Erythrocytes/cytology ; Erythrocytes/metabolism ; Glucosephosphate Dehydrogenase/metabolism ; Humans ; Metabolomics/methods ; Models, Molecular ; Oxidative Stress
Chemical Substances	Glucosephosphate Dehydrogenase (EC 1.1.1.49)
Language	English
Publishing date	2019-06-06
Publishing country	Italy
Document type	Journal Article ; Review
ZDB-ID	2135732-8
ISSN	2385-2070 ; 0041-1787 ; 1723-2007
ISSN (online)	2385-2070
ISSN	0041-1787 ; 1723-2007
DOI	10.2450/2019.0072-19
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