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Article ; Online: Elucidating Dynamics of Adenylate Kinase from Enzyme Opening to Ligand Release.

Nam, Kwangho / Arattu Thodika, Abdul Raafik / Grundström, Christin / Sauer, Uwe H / Wolf-Watz, Magnus

Journal of chemical information and modeling

2023 Volume 64, Issue 1, Page(s) 150–163

Abstract: This study explores ligand-driven conformational changes in adenylate kinase (AK), which is known for its open-to-close conformational transitions upon ligand binding and release. By utilizing string free energy simulations, we determine the free energy ... ...

Abstract	This study explores ligand-driven conformational changes in adenylate kinase (AK), which is known for its open-to-close conformational transitions upon ligand binding and release. By utilizing string free energy simulations, we determine the free energy profiles for both enzyme opening and ligand release and compare them with profiles from the apoenzyme. Results reveal a three-step ligand release process, which initiates with the opening of the adenosine triphosphate-binding subdomain (ATP lid), followed by ligand release and concomitant opening of the adenosine monophosphate-binding subdomain (AMP lid). The ligands then transition to nonspecific positions before complete dissociation. In these processes, the first step is energetically driven by ATP lid opening, whereas the second step is driven by ATP release. In contrast, the AMP lid opening and its ligand release make minor contributions to the total free energy for enzyme opening. Regarding the ligand binding mechanism, our results suggest that AMP lid closure occurs via an induced-fit mechanism triggered by AMP binding, whereas ATP lid closure follows conformational selection. This difference in the closure mechanisms provides an explanation with implications for the debate on ligand-driven conformational changes of AK. Additionally, we determine an X-ray structure of an AK variant that exhibits significant rearrangements in the stacking of catalytic arginines, explaining its reduced catalytic activity. In the context of apoenzyme opening, the sequence of events is different. Here, the AMP lid opens first while the ATP lid remains closed, and the free energy associated with ATP lid opening varies with orientation, aligning with the reported AK opening and closing rate heterogeneity. Finally, this study, in conjunction with our previous research, provides a comprehensive view of the intricate interplay between various structural elements, ligands, and catalytic residues that collectively contribute to the robust catalytic power of the enzyme.
MeSH term(s)	Adenylate Kinase/chemistry ; Ligands ; Apoenzymes/metabolism ; Adenosine Monophosphate/chemistry ; Adenosine Monophosphate/metabolism ; Adenosine Triphosphate/metabolism ; Protein Conformation
Chemical Substances	Adenylate Kinase (EC 2.7.4.3) ; Ligands ; Apoenzymes ; Adenosine Monophosphate (415SHH325A) ; Adenosine Triphosphate (8L70Q75FXE)
Language	English
Publishing date	2023-12-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	190019-5
ISSN	1549-960X ; 0095-2338
ISSN (online)	1549-960X
ISSN	0095-2338
DOI	10.1021/acs.jcim.3c01618
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Article ; Online: The Y233 gatekeeper of DmpR modulates effector-responsive transcriptional control of σ

Seibt, Henrik / Sauer, Uwe H / Shingler, Victoria

Environmental microbiology

2019 Volume 21, Issue 4, Page(s) 1321–1330

Abstract: DmpR is the obligate transcriptional activator of genes involved in (methyl)phenol catabolism by Pseudomonas putida. DmpR belongs to the ... ...

Abstract	DmpR is the obligate transcriptional activator of genes involved in (methyl)phenol catabolism by Pseudomonas putida. DmpR belongs to the AAA
MeSH term(s)	Adenosine Triphosphatases/metabolism ; Amino Acid Substitution ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Cresols/metabolism ; DNA-Directed RNA Polymerases/genetics ; DNA-Directed RNA Polymerases/metabolism ; Gene Expression Regulation, Bacterial ; Metabolism/genetics ; Protein Binding ; Pseudomonas putida/genetics ; Trans-Activators/metabolism ; Transcription Factors/genetics ; Transcriptional Activation/genetics
Chemical Substances	Bacterial Proteins ; Cresols ; DmpR protein, Pseudomonas ; Trans-Activators ; Transcription Factors ; DNA-Directed RNA Polymerases (EC 2.7.7.6) ; Adenosine Triphosphatases (EC 3.6.1.-) ; cresol (GF3CGH8D7Z)
Language	English
Publishing date	2019-03-07
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2020213-1
ISSN	1462-2920 ; 1462-2912
ISSN (online)	1462-2920
ISSN	1462-2912
DOI	10.1111/1462-2920.14567
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Article: Dynamic Connection between Enzymatic Catalysis and Collective Protein Motions

Ojeda-May, Pedro / Mushtaq, Ameeq UI / Rogne, Per / Verma, Apoorv / Ovchinnikov, Victor / Grundström, Christin / Dulko-Smith, Beata / Sauer, Uwe H. / Wolf-Watz, Magnus / Nam, Kwangho

Biochemistry. 2021 July 12, v. 60, no. 28

2021

Abstract: Enzymes employ a wide range of protein motions to achieve efficient catalysis of chemical reactions. While the role of collective protein motions in substrate binding, product release, and regulation of enzymatic activity is generally understood, their ... ...

Abstract	Enzymes employ a wide range of protein motions to achieve efficient catalysis of chemical reactions. While the role of collective protein motions in substrate binding, product release, and regulation of enzymatic activity is generally understood, their roles in catalytic steps per se remain uncertain. Here, molecular dynamics simulations, enzyme kinetics, X-ray crystallography, and nuclear magnetic resonance spectroscopy are combined to elucidate the catalytic mechanism of adenylate kinase and to delineate the roles of catalytic residues in catalysis and the conformational change in the enzyme. This study reveals that the motions in the active site, which occur on a time scale of picoseconds to nanoseconds, link the catalytic reaction to the slow conformational dynamics of the enzyme by modulating the free energy landscapes of subdomain motions. In particular, substantial conformational rearrangement occurs in the active site following the catalytic reaction. This rearrangement not only affects the reaction barrier but also promotes a more open conformation of the enzyme after the reaction, which then results in an accelerated opening of the enzyme compared to that of the reactant state. The results illustrate a linkage between enzymatic catalysis and collective protein motions, whereby the disparate time scales between the two processes are bridged by a cascade of intermediate-scale motion of catalytic residues modulating the free energy landscapes of the catalytic and conformational change processes.
Keywords	Gibbs free energy ; X-ray diffraction ; active sites ; adenylate kinase ; catalytic activity ; enzyme activity ; enzyme kinetics ; molecular dynamics ; nuclear magnetic resonance spectroscopy
Language	English
Dates of publication	2021-0712
Size	p. 2246-2258.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/acs.biochem.1c00221
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Article ; Online: Synthesis of Densely Functionalized

Singh, Pardeep / Cairns, Andrew G / Adolfsson, Dan E / Ådén, Jörgen / Sauer, Uwe H / Almqvist, Fredrik

Organic letters

2019 Volume 21, Issue 17, Page(s) 6946–6950

Abstract: We report the synthesis of 6-arylthio-substituted- ...

Abstract	We report the synthesis of 6-arylthio-substituted-
MeSH term(s)	Benzene Derivatives/chemistry ; Cycloaddition Reaction ; Molecular Structure ; Pyridones/chemical synthesis ; Pyridones/chemistry ; Thiazoles/chemistry
Chemical Substances	Benzene Derivatives ; Pyridones ; Thiazoles ; benzyne ; 2-hydroxypyridine (6770O3A2I5)
Language	English
Publishing date	2019-08-16
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	1523-7052
ISSN (online)	1523-7052
DOI	10.1021/acs.orglett.9b02549
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Article: Synthesis of Densely Functionalized N-Alkenyl 2-Pyridones via Benzyne-Induced Ring Opening of Thiazolino-Fused 2-Pyridones

Singh, Pardeep / Cairns, Andrew G / Adolfsson, Dan E / Ådén, Jörgen / Sauer, Uwe H / Almqvist, Fredrik

Organic letters. 2019 Aug. 16, v. 21, no. 17

2019

Abstract: We report the synthesis of 6-arylthio-substituted-N-alkenyl 2-pyridones by ring opening of bicyclic thiazolino-2-pyridones with arynes. Varied functionalization was used to investigate scope and substituent influences on reactivity. Selected conditions ... ...

Abstract	We report the synthesis of 6-arylthio-substituted-N-alkenyl 2-pyridones by ring opening of bicyclic thiazolino-2-pyridones with arynes. Varied functionalization was used to investigate scope and substituent influences on reactivity. Selected conditions favor thioether ring opening over [4 + 2] cycloaddition and an unusual aryne incorporating ring expansion. Deuterium labeling was used to clarify observed reactivity. Using the knowledge, we produced drug-like molecules with complex substitution patterns and show how thioether ring opening can be used on scaffolds with competing reactivities.
Keywords	chemical structure ; cycloaddition reactions ; deuterium ; organic compounds
Language	English
Dates of publication	2019-0816
Size	p. 6946-6950.
Publishing place	American Chemical Society
Document type	Article
ISSN	1523-7052
DOI	10.1021/acs.orglett.9b02549
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Article ; Online: Insights into the evolution of enzymatic specificity and catalysis: From Asgard archaea to human adenylate kinases.

Verma, Apoorv / Åberg-Zingmark, Emma / Sparrman, Tobias / Mushtaq, Ameeq Ul / Rogne, Per / Grundström, Christin / Berntsson, Ronnie / Sauer, Uwe H / Backman, Lars / Nam, Kwangho / Sauer-Eriksson, Elisabeth / Wolf-Watz, Magnus

Science advances

2022 Volume 8, Issue 44, Page(s) eabm4089

Abstract: Enzymatic catalysis is critically dependent on selectivity, active site architecture, and dynamics. To contribute insights into the interplay of these properties, we established an approach with NMR, crystallography, and MD simulations focused on the ... ...

Abstract	Enzymatic catalysis is critically dependent on selectivity, active site architecture, and dynamics. To contribute insights into the interplay of these properties, we established an approach with NMR, crystallography, and MD simulations focused on the ubiquitous phosphotransferase adenylate kinase (AK) isolated from Odinarchaeota (OdinAK). Odinarchaeota belongs to the Asgard archaeal phylum that is believed to be the closest known ancestor to eukaryotes. We show that OdinAK is a hyperthermophilic trimer that, contrary to other AK family members, can use all NTPs for its phosphorylation reaction. Crystallographic structures of OdinAK-NTP complexes revealed a universal NTP-binding motif, while <sup>19</sup>F NMR experiments uncovered a conserved and rate-limiting dynamic signature. As a consequence of trimerization, the active site of OdinAK was found to be lacking a critical catalytic residue and is therefore considered to be "atypical." On the basis of discovered relationships with human monomeric homologs, our findings are discussed in terms of evolution of enzymatic substrate specificity and cold adaptation.
MeSH term(s)	Humans ; Archaea/genetics ; Adenylate Kinase/chemistry ; Catalysis ; Catalytic Domain
Chemical Substances	Adenylate Kinase (EC 2.7.4.3)
Language	English
Publishing date	2022-11-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	2810933-8
ISSN	2375-2548 ; 2375-2548
ISSN (online)	2375-2548
ISSN	2375-2548
DOI	10.1126/sciadv.abm4089
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Article ; Online: Molecular mechanism of ATP versus GTP selectivity of adenylate kinase.

Rogne, Per / Rosselin, Marie / Grundström, Christin / Hedberg, Christian / Sauer, Uwe H / Wolf-Watz, Magnus

Proceedings of the National Academy of Sciences of the United States of America

2018 Volume 115, Issue 12, Page(s) 3012–3017

Abstract: Enzymatic substrate selectivity is critical for the precise control of metabolic pathways. In cases where chemically related substrates are present inside cells, robust mechanisms of substrate selectivity are required. Here, we report the mechanism ... ...

Abstract	Enzymatic substrate selectivity is critical for the precise control of metabolic pathways. In cases where chemically related substrates are present inside cells, robust mechanisms of substrate selectivity are required. Here, we report the mechanism utilized for catalytic ATP versus GTP selectivity during adenylate kinase (Adk) -mediated phosphorylation of AMP. Using NMR spectroscopy we found that while Adk adopts a catalytically competent and closed structural state in complex with ATP, the enzyme is arrested in a catalytically inhibited and open state in complex with GTP. X-ray crystallography experiments revealed that the interaction interfaces supporting ATP and GTP recognition, in part, are mediated by coinciding residues. The mechanism provides an atomic view on how the cellular GTP pool is protected from Adk turnover, which is important because GTP has many specialized cellular functions. In further support of this mechanism, a structure-function analysis enabled by synthesis of ATP analogs suggests that a hydrogen bond between the adenine moiety and the backbone of the enzyme is vital for ATP selectivity. The importance of the hydrogen bond for substrate selectivity is likely general given the conservation of its location and orientation across the family of eukaryotic protein kinases.
MeSH term(s)	Adenosine Triphosphate/metabolism ; Adenylyl Cyclase Inhibitors/chemistry ; Adenylyl Cyclase Inhibitors/pharmacology ; Adenylyl Cyclases/metabolism ; Guanosine Triphosphate/metabolism ; Inosine Triphosphate/genetics ; Inosine Triphosphate/metabolism ; Kinetics ; Models, Molecular ; Protein Conformation ; Structure-Activity Relationship ; Substrate Specificity
Chemical Substances	Adenylyl Cyclase Inhibitors ; Inosine Triphosphate (132-06-9) ; Guanosine Triphosphate (86-01-1) ; Adenosine Triphosphate (8L70Q75FXE) ; Adenylyl Cyclases (EC 4.6.1.1)
Language	English
Publishing date	2018-03-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1721508115
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Article ; Online: Dynamic Connection between Enzymatic Catalysis and Collective Protein Motions.

Ojeda-May, Pedro / Mushtaq, Ameeq Ui / Rogne, Per / Verma, Apoorv / Ovchinnikov, Victor / Grundström, Christin / Dulko-Smith, Beata / Sauer, Uwe H / Wolf-Watz, Magnus / Nam, Kwangho

Biochemistry

2021 Volume 60, Issue 28, Page(s) 2246–2258

Abstract	Enzymes employ a wide range of protein motions to achieve efficient catalysis of chemical reactions. While the role of collective protein motions in substrate binding, product release, and regulation of enzymatic activity is generally understood, their roles in catalytic steps per se remain uncertain. Here, molecular dynamics simulations, enzyme kinetics, X-ray crystallography, and nuclear magnetic resonance spectroscopy are combined to elucidate the catalytic mechanism of adenylate kinase and to delineate the roles of catalytic residues in catalysis and the conformational change in the enzyme. This study reveals that the motions in the active site, which occur on a time scale of picoseconds to nanoseconds, link the catalytic reaction to the slow conformational dynamics of the enzyme by modulating the free energy landscapes of subdomain motions. In particular, substantial conformational rearrangement occurs in the active site following the catalytic reaction. This rearrangement not only affects the reaction barrier but also promotes a more open conformation of the enzyme after the reaction, which then results in an accelerated opening of the enzyme compared to that of the reactant state. The results illustrate a linkage between enzymatic catalysis and collective protein motions, whereby the disparate time scales between the two processes are bridged by a cascade of intermediate-scale motion of catalytic residues modulating the free energy landscapes of the catalytic and conformational change processes.
MeSH term(s)	Adenylate Kinase/chemistry ; Catalytic Domain ; Crystallography, X-Ray ; Escherichia coli/chemistry ; Escherichia coli/enzymology ; Escherichia coli Proteins/chemistry ; Molecular Dynamics Simulation ; Protein Conformation
Chemical Substances	Escherichia coli Proteins ; Adenylate Kinase (EC 2.7.4.3)
Language	English
Publishing date	2021-07-12
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/acs.biochem.1c00221
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Article ; Online: Structural basis for ligand binding to an enzyme by a conformational selection pathway.

Kovermann, Michael / Grundström, Christin / Sauer-Eriksson, A Elisabeth / Sauer, Uwe H / Wolf-Watz, Magnus

Proceedings of the National Academy of Sciences of the United States of America

2017 Volume 114, Issue 24, Page(s) 6298–6303

Abstract: Proteins can bind target molecules through either induced fit or conformational selection pathways. In the conformational selection model, a protein samples a scarcely populated high-energy state that resembles a target-bound conformation. In enzymatic ... ...

Abstract	Proteins can bind target molecules through either induced fit or conformational selection pathways. In the conformational selection model, a protein samples a scarcely populated high-energy state that resembles a target-bound conformation. In enzymatic catalysis, such high-energy states have been identified as crucial entities for activity and the dynamic interconversion between ground states and high-energy states can constitute the rate-limiting step for catalytic turnover. The transient nature of these states has precluded direct observation of their properties. Here, we present a molecular description of a high-energy enzyme state in a conformational selection pathway by an experimental strategy centered on NMR spectroscopy, protein engineering, and X-ray crystallography. Through the introduction of a disulfide bond, we succeeded in arresting the enzyme adenylate kinase in a closed high-energy conformation that is on-pathway for catalysis. A 1.9-Å X-ray structure of the arrested enzyme in complex with a transition state analog shows that catalytic sidechains are properly aligned for catalysis. We discovered that the structural sampling of the substrate free enzyme corresponds to the complete amplitude that is associated with formation of the closed and catalytically active state. In addition, we found that the trapped high-energy state displayed improved ligand binding affinity, compared with the wild-type enzyme, demonstrating that substrate binding to the high-energy state is not occluded by steric hindrance. Finally, we show that quenching of fast time scale motions observed upon ligand binding to adenylate kinase is dominated by enzyme-substrate interactions and not by intramolecular interactions resulting from the conformational change.
Language	English
Publishing date	2017-06-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1700919114
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Article ; Online: Targeting the Main Protease (M

Altincekic, Nadide / Jores, Nathalie / Löhr, Frank / Richter, Christian / Ehrhardt, Claus / Blommers, Marcel J J / Berg, Hannes / Öztürk, Sare / Gande, Santosh L / Linhard, Verena / Orts, Julien / Abi Saad, Marie Jose / Bütikofer, Matthias / Kaderli, Janina / Karlsson, B Göran / Brath, Ulrika / Hedenström, Mattias / Gröbner, Gerhard / Sauer, Uwe H /

Perrakis, Anastassis / Langer, Julian / Banci, Lucia / Cantini, Francesca / Fragai, Marco / Grifagni, Deborah / Barthel, Tatjana / Wollenhaupt, Jan / Weiss, Manfred S / Robertson, Angus / Bax, Adriaan / Sreeramulu, Sridhar / Schwalbe, Harald

ACS chemical biology

2024 Volume 19, Issue 2, Page(s) 563–574

Abstract: The main protease ... ...

Abstract	The main protease M
MeSH term(s)	Drug Discovery/methods ; SARS-CoV-2/metabolism ; Catalytic Domain ; Magnetic Resonance Spectroscopy ; Peptide Hydrolases/metabolism ; Protease Inhibitors/metabolism ; Antiviral Agents/pharmacology ; Molecular Docking Simulation
Chemical Substances	Peptide Hydrolases (EC 3.4.-) ; Protease Inhibitors ; Antiviral Agents
Language	English
Publishing date	2024-01-17
Publishing country	United States
Document type	Journal Article
ISSN	1554-8937
ISSN (online)	1554-8937
DOI	10.1021/acschembio.3c00720
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