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Article ; Online: The Protein Microenvironment Governs the Suitability of Labeling Sites for Single-Molecule Spectroscopy of RNP Complexes.

Schmidt, Andreas / Altincekic, Nadide / Gustmann, Henrik / Wachtveitl, Josef / Hengesbach, Martin

ACS chemical biology

2018 Volume 13, Issue 9, Page(s) 2472–2483

Abstract: Single-molecule techniques allow unique insights into biological systems as they provide unrivaled access to structural dynamics and conformational heterogeneity. One major bottleneck for reliable single-molecule Förster resonance energy transfer (smFRET) ...

Abstract	Single-molecule techniques allow unique insights into biological systems as they provide unrivaled access to structural dynamics and conformational heterogeneity. One major bottleneck for reliable single-molecule Förster resonance energy transfer (smFRET) analysis is the identification of suitable fluorophore labeling sites that neither impair the function of the biological system nor cause photophysical artifacts of the fluorophore. To address this issue, we identified the contribution of virtually all individual parameters that affect Förster resonance energy transfer between two fluorophores attached to a ribonucleoprotein complex consisting of the RNA-binding protein L7Ae and a cognate kink turn containing RNA. A non-natural amino acid was incorporated at various positions of the protein using an amber suppression system (pEVOL) to label the protein via copper(I)-catalyzed alkyne-azide cycloaddition. On the basis of simulations followed by functional, structural, and multiparameter fluorescence analysis of five different smFRET RNPs, new insights into the design of smFRET RNPs were obtained. From this, a correlation between the photophysical properties of fluorophores attached to the protein and the predictability of the corresponding smFRET construct was established. Additionally, we identify a straightforward experimental method for characterizing selected labeling sites. Overall, this protocol allows fast generation and assessment of functional RNPs for accurate single-molecule experiments.
MeSH term(s)	Bacterial Proteins/chemistry ; Fluorescence ; Fluorescence Resonance Energy Transfer/methods ; Fluorescent Dyes/chemistry ; Models, Molecular ; Pyrococcus furiosus/chemistry ; RNA/chemistry ; Ribonucleoproteins/chemistry
Chemical Substances	Bacterial Proteins ; Fluorescent Dyes ; Ribonucleoproteins ; RNA (63231-63-0)
Language	English
Publishing date	2018-08-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1554-8937
ISSN (online)	1554-8937
DOI	10.1021/acschembio.8b00348
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Site-Specific Detection of Arginine Methylation in Highly Repetitive Protein Motifs of Low Sequence Complexity by NMR

Altincekic, Nadide / Löhr, Frank / Meier-Credo, Jakob / Langer, Julian D / Hengesbach, Martin / Richter, Christian / Schwalbe, Harald

Journal of the American Chemical Society. 2020 Apr. 01, v. 142, no. 16

2020

Abstract: Post-translational modifications of proteins are widespread in eukaryotes. To elucidate the functional role of these modifications, detection methods need to be developed that provide information at atomic resolution. Here, we report on the development ... ...

Abstract	Post-translational modifications of proteins are widespread in eukaryotes. To elucidate the functional role of these modifications, detection methods need to be developed that provide information at atomic resolution. Here, we report on the development of a novel Arg-specific NMR experiment that detects the methylation status and symmetry of each arginine side chain even in highly repetitive RGG amino acid sequence motifs found in numerous proteins within intrinsically disordered regions. The experiment relies on the excellent resolution of the backbone H,N correlation spectra even in these low complexity sequences. It requires ¹³C, ¹⁵N labeled samples.
Keywords	amino acid motifs ; arginine ; carbon ; eukaryotic cells ; isotope labeling ; methylation ; nuclear magnetic resonance spectroscopy ; post-translational modification ; proteins ; stable isotopes
Language	English
Dates of publication	2020-0401
Size	p. 7647-7654.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.0c02308
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Article ; Online: Nano-Differential Scanning Fluorimetry for Screening in Fragment-based Lead Discovery.

Ahmad, Misbha Ud Din / Fish, Alexander / Molenaar, Jeroen / Sreeramulu, Sridhar / Richter, Christian / Altincekic, Nadide / Schwalbe, Harald / Wienk, Hans / Perrakis, Anastassis

Journal of visualized experiments : JoVE

2021 , Issue 171

Abstract: Thermal shift assays (TSAs) examine how the melting temperature (Tm) of a target protein changes in response to changes in its environment (e.g., buffer composition). The utility of TSA, and specifically of nano-Differential Scanning Fluorimetry (nano- ... ...

Abstract	Thermal shift assays (TSAs) examine how the melting temperature (Tm) of a target protein changes in response to changes in its environment (e.g., buffer composition). The utility of TSA, and specifically of nano-Differential Scanning Fluorimetry (nano-DSF), has been established over the years, both for finding conditions that help stabilize a specific protein and for looking at ligand binding by monitoring changes in the apparent Tm. This paper presents an efficient screening of the Diamond-SGC-iNEXT Poised (DSi-Poised) fragment library (768 compounds) by the use of nano-DSF, monitoring Tm to identify potential fragment binding. The prerequisites regarding protein quality and concentration for performing nano-DSF experiments are briefly outlined followed by a step-by-step protocol that uses a nano-liter robotic dispenser commonly used in structural biology laboratories for preparing the required samples in 96-well plates. The protocol describes how the reagent mixtures are transferred to the capillaries needed for nano-DSF measurements. In addition, this paper provides protocols to measure thermal denaturation (monitoring intrinsic tryptophan fluorescence) and aggregation (monitoring light back-scattering) and the subsequent steps for data transfer and analysis. Finally, screening experiments with three different protein targets are discussed to illustrate the use of this procedure in the context of lead discovery campaigns. The overall principle of the method described can be easily transferred to other fragment libraries or adapted to other instruments.
MeSH term(s)	Fluorometry ; Proteins ; Temperature
Chemical Substances	Proteins
Language	English
Publishing date	2021-05-16
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Video-Audio Media
ZDB-ID	2259946-0
ISSN	1940-087X ; 1940-087X
ISSN (online)	1940-087X
ISSN	1940-087X
DOI	10.3791/62469
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Article: Nano-differential scanning fluorimetry for screening in fragment-based lead discovery

Ahmad, Misbha Ud Din / Fish, Alexander / Molenaar, Jeroen / Sreeramulu, Sridhar / Richter, Christian / Altincekic, Nadide / Schwalbe, Harald / Wienk, Hans / Perrakis, Anastassis

Journal of visualized experiments. 2021 May 16, , no. 171

2021

Abstract	Thermal shift assays (TSAs) examine how the melting temperature (Tm) of a target protein changes in response to changes in its environment (e.g., buffer composition). The utility of TSA, and specifically of nano-Differential Scanning Fluorimetry (nano-DSF), has been established over the years, both for finding conditions that help stabilize a specific protein and for looking at ligand binding by monitoring changes in the apparent Tm. This paper presents an efficient screening of the Diamond-SGC-iNEXT Poised (DSi-Poised) fragment library (768 compounds) by the use of nano-DSF, monitoring Tm to identify potential fragment binding. The prerequisites regarding protein quality and concentration for performing nano-DSF experiments are briefly outlined followed by a step-by-step protocol that uses a nano-liter robotic dispenser commonly used in structural biology laboratories for preparing the required samples in 96-well plates. The protocol describes how the reagent mixtures are transferred to the capillaries needed for nano-DSF measurements. In addition, this paper provides protocols to measure thermal denaturation (monitoring intrinsic tryptophan fluorescence) and aggregation (monitoring light back-scattering) and the subsequent steps for data transfer and analysis. Finally, screening experiments with three different protein targets are discussed to illustrate the use of this procedure in the context of lead discovery campaigns. The overall principle of the method described can be easily transferred to other fragment libraries or adapted to other instruments.
Keywords	denaturation ; fluorescence ; fluorometry ; ligands ; protein value ; robots ; structural biology ; temperature ; tryptophan
Language	English
Dates of publication	2021-0516
Size	p. e62469.
Publishing place	Journal of Visualized Experiments
Document type	Article
ZDB-ID	2259946-0
ISSN	1940-087X
ISSN	1940-087X
DOI	10.3791/62469
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Article ; Online: Site-Specific Detection of Arginine Methylation in Highly Repetitive Protein Motifs of Low Sequence Complexity by NMR.

Altincekic, Nadide / Löhr, Frank / Meier-Credo, Jakob / Langer, Julian D / Hengesbach, Martin / Richter, Christian / Schwalbe, Harald

Journal of the American Chemical Society

2020 Volume 142, Issue 16, Page(s) 7647–7654

Abstract	Post-translational modifications of proteins are widespread in eukaryotes. To elucidate the functional role of these modifications, detection methods need to be developed that provide information at atomic resolution. Here, we report on the development of a novel Arg-specific NMR experiment that detects the methylation status and symmetry of each arginine side chain even in highly repetitive RGG amino acid sequence motifs found in numerous proteins within intrinsically disordered regions. The experiment relies on the excellent resolution of the backbone H,N correlation spectra even in these low complexity sequences. It requires
MeSH term(s)	Arginine/chemistry ; Humans ; Magnetic Resonance Spectroscopy/methods ; Methylation ; Proteins/chemistry
Chemical Substances	Proteins ; Arginine (94ZLA3W45F)
Language	English
Publishing date	2020-04-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.0c02308
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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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Article ; Online: Binding Adaptation of GS-441524 Diversifies Macro Domains and Downregulates SARS-CoV-2 de-MARylation Capacity.

Tsika, Aikaterini C / Gallo, Angelo / Fourkiotis, Nikolaos K / Argyriou, Aikaterini I / Sreeramulu, Sridhar / Löhr, Frank / Rogov, Vladimir V / Richter, Christian / Linhard, Verena / Gande, Santosh L / Altincekic, Nadide / Krishnathas, Robin / Elamri, Isam / Schwalbe, Harald / Wollenhaupt, Jan / Weiss, Manfred S / Spyroulias, Georgios A

Journal of molecular biology

2022 Volume 434, Issue 16, Page(s) 167720

Abstract: Viral infection in cells triggers a cascade of molecular defense mechanisms to maintain host-cell homoeostasis. One of these mechanisms is ADP-ribosylation, a fundamental post-translational modification (PTM) characterized by the addition of ADP-ribose ( ... ...

Abstract	Viral infection in cells triggers a cascade of molecular defense mechanisms to maintain host-cell homoeostasis. One of these mechanisms is ADP-ribosylation, a fundamental post-translational modification (PTM) characterized by the addition of ADP-ribose (ADPr) on substrates. Poly(ADP-ribose) polymerases (PARPs) are implicated in this process and they perform ADP-ribosylation on host and pathogen proteins. Some viral families contain structural motifs that can reverse this PTM. These motifs known as macro domains (MDs) are evolutionarily conserved protein domains found in all kingdoms of life. They are divided in different classes with the viral belonging to Macro-D-type class because of their properties to recognize and revert the ADP-ribosylation. Viral MDs are potential pharmaceutical targets, capable to counteract host immune response. Sequence and structural homology between viral and human MDs are an impediment for the development of new active compounds against their function. Remdesivir, is a drug administrated in viral infections inhibiting viral replication through RNA-dependent RNA polymerase (RdRp). Herein, GS-441524, the active metabolite of the remdesivir, is tested as a hydrolase inhibitor for several viral MDs and for its binding to human homologs found in PARPs. This study presents biochemical and biophysical studies, which indicate that GS-441524 selectively modifies SARS-CoV-2 MD de-MARylation activity, while it does not interact with hPARP14 MD2 and hPARP15 MD2. The structural investigation of MD•GS-441524 complexes, using solution NMR and X-ray crystallography, discloses the impact of certain amino acids in ADPr binding cavity suggesting that F360 and its adjacent residues tune the selective binding of the inhibitor to SARS-CoV-2 MD.
MeSH term(s)	ADP-Ribosylation/drug effects ; Adenosine/analogs & derivatives ; Adenosine/chemistry ; Adenosine/pharmacology ; Adenosine Diphosphate Ribose/chemistry ; Coronavirus Protease Inhibitors/chemistry ; Coronavirus Protease Inhibitors/pharmacology ; Humans ; Poly(ADP-ribose) Polymerases/chemistry ; Protein Binding ; Protein Domains ; SARS-CoV-2/drug effects ; SARS-CoV-2/enzymology
Chemical Substances	Coronavirus Protease Inhibitors ; GS-441524 (1BQK176DT6) ; Adenosine Diphosphate Ribose (20762-30-5) ; Poly(ADP-ribose) Polymerases (EC 2.4.2.30) ; Adenosine (K72T3FS567)
Language	English
Publishing date	2022-07-15
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2022.167720
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Article ; Online: Binding Adaptation of GS-441524 Diversifies Macro Domains and Downregulates SARS-CoV-2 de-MARylation Capacity

Tsika, Aikaterini C. / Gallo, Angelo / Fourkiotis, Nikolaos K. / Argyriou, Aikaterini I. / Sreeramulu, Sridhar / Löhr, Frank / Rogov, Vladimir V. / Richter, Christian / Linhard, Verena / Gande, Santosh L. / Altincekic, Nadide / Krishnathas, Robin / Elamri, Isam / Schwalbe, Harald / Wollenhaupt, Jan / Weiss, Manfred S. / Spyroulias, Georgios A.

Journal of Molecular Biology. 2022 Aug., v. 434, no. 16 p.167720-

2022

Abstract	Viral infection in cells triggers a cascade of molecular defense mechanisms to maintain host-cell homoeostasis. One of these mechanisms is ADP-ribosylation, a fundamental post-translational modification (PTM) characterized by the addition of ADP-ribose (ADPr) on substrates. Poly(ADP-ribose) polymerases (PARPs) are implicated in this process and they perform ADP-ribosylation on host and pathogen proteins. Some viral families contain structural motifs that can reverse this PTM. These motifs known as macro domains (MDs) are evolutionarily conserved protein domains found in all kingdoms of life. They are divided in different classes with the viral belonging to Macro-D-type class because of their properties to recognize and revert the ADP-ribosylation. Viral MDs are potential pharmaceutical targets, capable to counteract host immune response. Sequence and structural homology between viral and human MDs are an impediment for the development of new active compounds against their function. Remdesivir, is a drug administrated in viral infections inhibiting viral replication through RNA-dependent RNA polymerase (RdRp). Herein, GS-441524, the active metabolite of the remdesivir, is tested as a hydrolase inhibitor for several viral MDs and for its binding to human homologs found in PARPs. This study presents biochemical and biophysical studies, which indicate that GS-441524 selectively modifies SARS-CoV-2 MD de-MARylation activity, while it does not interact with hPARP14 MD2 and hPARP15 MD2. The structural investigation of MD•GS-441524 complexes, using solution NMR and X-ray crystallography, discloses the impact of certain amino acids in ADPr binding cavity suggesting that F360 and its adjacent residues tune the selective binding of the inhibitor to SARS-CoV-2 MD.
Keywords	RNA-directed RNA polymerase ; Severe acute respiratory syndrome coronavirus 2 ; drugs ; humans ; hydrolases ; immune response ; metabolites ; molecular biology ; pathogens ; post-translational modification ; virus replication ; Remdesivir ; ADP-ribosylation ; PARPs ; Coronaviruses ; Alphaviruses ; Macro domain ; SARS-CoV-2 ; SARS-CoV-1 ; MERS-CoV ; CHIKV ; MAYV ; VEEV ; ADPr ; ART ; PARP ; CoV ; MD ; NAD
Language	English
Dates of publication	2022-08
Publishing place	Elsevier Ltd
Document type	Article ; Online
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2022.167720
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Article ; Online: 1

Vögele, Jennifer / Ferner, Jan-Peter / Altincekic, Nadide / Bains, Jasleen Kaur / Ceylan, Betül / Fürtig, Boris / Grün, J Tassilo / Hengesbach, Martin / Hohmann, Katharina F / Hymon, Daniel / Knezic, Bozana / Löhr, Frank / Peter, Stephen A / Pyper, Dennis / Qureshi, Nusrat S / Richter, Christian / Schlundt, Andreas / Schwalbe, Harald / Stirnal, Elke /

Sudakov, Alexey / Wacker, Anna / Weigand, Julia E / Wirmer-Bartoschek, Julia / Wöhnert, Jens / Duchardt-Ferner, Elke

Biomolecular NMR assignments

2021 Volume 15, Issue 2, Page(s) 335–340

Abstract: The SARS-CoV-2 virus is the cause of the respiratory disease COVID-19. As of today, therapeutic interventions in severe COVID-19 cases are still not available as no effective therapeutics have been developed so far. Despite the ongoing development of a ... ...

Abstract	The SARS-CoV-2 virus is the cause of the respiratory disease COVID-19. As of today, therapeutic interventions in severe COVID-19 cases are still not available as no effective therapeutics have been developed so far. Despite the ongoing development of a number of effective vaccines, therapeutics to fight the disease once it has been contracted will still be required. Promising targets for the development of antiviral agents against SARS-CoV-2 can be found in the viral RNA genome. The 5'- and 3'-genomic ends of the 30 kb SCoV-2 genome are highly conserved among Betacoronaviruses and contain structured RNA elements involved in the translation and replication of the viral genome. The 40 nucleotides (nt) long highly conserved stem-loop 4 (5_SL4) is located within the 5'-untranslated region (5'-UTR) important for viral replication. 5_SL4 features an extended stem structure disrupted by several pyrimidine mismatches and is capped by a pentaloop. Here, we report extensive
MeSH term(s)	5' Untranslated Regions ; Inverted Repeat Sequences/genetics ; Nuclear Magnetic Resonance, Biomolecular ; SARS-CoV-2/genetics
Chemical Substances	5' Untranslated Regions
Language	English
Publishing date	2021-04-29
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2388861-1
ISSN	1874-270X ; 1874-2718
ISSN (online)	1874-270X
ISSN	1874-2718
DOI	10.1007/s12104-021-10026-7
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Article ; Online: 1

Mertinkus, Klara R / Grün, J Tassilo / Altincekic, Nadide / Bains, Jasleen Kaur / Ceylan, Betül / Ferner, Jan-Peter / Frydman, Lucio / Fürtig, Boris / Hengesbach, Martin / Hohmann, Katharina F / Hymon, Daniel / Kim, Jihyun / Knezic, Božana / Novakovic, Mihajlo / Oxenfarth, Andreas / Peter, Stephen A / Qureshi, Nusrat S / Richter, Christian / Scherf, Tali /

Schlundt, Andreas / Schnieders, Robbin / Schwalbe, Harald / Stirnal, Elke / Sudakov, Alexey / Vögele, Jennifer / Wacker, Anna / Weigand, Julia E / Wirmer-Bartoschek, Julia / Martin, Maria A Wirtz / Wöhnert, Jens

Biomolecular NMR assignments

2022 Volume 16, Issue 1, Page(s) 17–25

Abstract: The ongoing pandemic of the respiratory disease COVID-19 is caused by the SARS-CoV-2 (SCoV2) virus. SCoV2 is a member of the Betacoronavirus genus. The 30 kb positive sense, single stranded RNA genome of SCoV2 features 5'- and 3'-genomic ends that are ... ...

Abstract	The ongoing pandemic of the respiratory disease COVID-19 is caused by the SARS-CoV-2 (SCoV2) virus. SCoV2 is a member of the Betacoronavirus genus. The 30 kb positive sense, single stranded RNA genome of SCoV2 features 5'- and 3'-genomic ends that are highly conserved among Betacoronaviruses. These genomic ends contain structured cis-acting RNA elements, which are involved in the regulation of viral replication and translation. Structural information about these potential antiviral drug targets supports the development of novel classes of therapeutics against COVID-19. The highly conserved branched stem-loop 5 (SL5) found within the 5'-untranslated region (5'-UTR) consists of a basal stem and three stem-loops, namely SL5a, SL5b and SL5c. Both, SL5a and SL5b feature a 5'-UUUCGU-3' hexaloop that is also found among Alphacoronaviruses. Here, we report the extensive
MeSH term(s)	5' Untranslated Regions ; COVID-19 ; Humans ; Magnetic Resonance Spectroscopy ; Nuclear Magnetic Resonance, Biomolecular ; SARS-CoV-2
Chemical Substances	5' Untranslated Regions
Language	English
Publishing date	2022-02-18
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2388861-1
ISSN	1874-270X ; 1874-2718
ISSN (online)	1874-270X
ISSN	1874-2718
DOI	10.1007/s12104-021-10053-4
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