| 1. |
- Agback, Peter, et al.
(författare)
-
H-1, C-13 and N-15 resonance assignment of backbone and IVL-methyl side chain of the S135A mutant NS3pro/NS2B protein of Dengue II virus reveals unique secondary structure features in solution
- 2022
-
Ingår i: Biomolecular Nmr Assignments. - : Springer Science and Business Media LLC. - 1874-2718 .- 1874-270X. ; 16, s. 135-145
-
Tidskriftsartikel (refereegranskat)abstract
- The serotype II Dengue (DENV 2) virus is the most prevalent of all four known serotypes. Herein, we present nearly complete H-1, N-15, and C-13 backbone and H-1, C-13 isoleucine, valine, and leucine methyl resonance assignment of the apo S135A catalytically inactive variant of the DENV 2 protease enzyme folded as a tandem formed between the serine protease domain NS3pro and the cofactor NS2B, as well as the secondary structure prediction of this complex based on the assigned chemical shifts using the TALOS-N software. Our results provide a solid ground for future elucidation of the structure and dynamic of the apo NS3pro/NS2B complex, key for adequate development of inhibitors, and a thorough molecular understanding of their function(s).
|
|
| 2. |
- Amorim, Gisele C, et al.
(författare)
-
¹H, ¹⁵N and ¹³C resonance assignments of PpdD, a type IV pilin from enterohemorrhagic Escherichia coli
- 2014
-
Ingår i: Biomolecular NMR Assignments. - : Springer Science and Business Media LLC. - 1874-2718 .- 1874-270X. ; 8:1, s. 43-46
-
Tidskriftsartikel (refereegranskat)abstract
- Bacterial type 4 pili (T4P) are long flexible fibers involved in adhesion, DNA uptake, phage transduction, aggregation and a flagella-independent movement called "twitching motility". T4P comprise thousands of copies of the major pilin subunit, which is initially inserted in the plasma membrane, processed and assembled into dynamic helical filaments. T4P are crucial for host colonization and virulence of many Gram-negative bacteria. In enterohemorrhagic Escherichia coli the T4P, called hemorrhagic coli pili (HCP) promote cell adhesion, motility, biofilm formation and signaling. To understand the mechanism of HCP assembly and function, we analyzed the structure of the major subunit prepilin peptidase-dependent protein D (PpdD) (also called HcpA), a 15 kDa pilin with two potential disulfide bonds. Here we present the (1)H, (15)N and (13)C backbone and side chain resonance assignments of the C-terminal globular domain of PpdD as a first step to its structural determination.
|
|
| 3. |
- Bobay, Benjamin G, et al.
(författare)
-
Chemical shift assignments and secondary structure prediction of the phosphorelay protein VanU from Vibrio anguillarum
- 2014
-
Ingår i: Biomolecular NMR Assignments. - : Springer Netherlands. - 1874-2718 .- 1874-270X. ; 8:1, s. 177-179
-
Tidskriftsartikel (refereegranskat)abstract
- Vibrio anguillarum is a biofilm forming Gram-negative bacterium that survives prolonged periods in seawater and causes vibriosis in marine life. A quorum-sensing signal transduction pathway initiates biofilm formation in response to environmental stresses. The phosphotransferase protein VanU is the focal point of the quorum-sensing pathway and facilitates the regulation between independent phosphorelay systems that activate or repress biofilm formation. Here we report the (1)H, (13)C, and (15)N backbone and side chain resonance assignments and secondary structure prediction for VanU from V. anguillarum.
|
|
| 4. |
- Born, Alexandra, et al.
(författare)
-
Backbone and side-chain chemical shift assignments of full-length, apo, human Pin1, a phosphoprotein regulator with interdomain allostery
- 2019
-
Ingår i: Biomolecular NMR Assignments. - : SPRINGER. - 1874-2718 .- 1874-270X. ; 13:1, s. 85-89
-
Tidskriftsartikel (refereegranskat)abstract
- Pin1 is a human peptidyl-prolyl cis-trans isomerase important for the regulation of phosphoproteins that are implicated in many diseases including cancer and Alzheimer's. Further biophysical study of Pin1 will elucidate the importance of the two-domain system to regulate its own activity. Here, we report near-complete backbone and side-chain H-1, C-13 and N-15 NMR chemical shift assignments of full-length, apo Pin1 for the purpose of studying interdomain allostery and dynamics.
|
|
| 5. |
|
|
| 6. |
- Han, X., et al.
(författare)
-
Assignment of IVL-Methyl side chain of the ligand-free monomeric human MALT1 paracaspase-IgL(3) domain in solution
- 2022
-
Ingår i: Biomolecular Nmr Assignments. - : Springer Science and Business Media LLC. - 1874-2718 .- 1874-270X. ; 16:2, s. 363-371
-
Tidskriftsartikel (refereegranskat)abstract
- Mucosa-associated lymphoid tissue protein 1 (MALT1) plays a key role in adaptive immune responses by modulating specific intracellular signalling pathways that control the development and proliferation of both T and B cells. Dysfunction of these pathways is coupled to the progress of highly aggressive lymphoma as well as to potential development of an array of different immune disorders. In contrast to other signalling mediators, MALT1 is not only activated through the formation of the CBM complex together with the proteins CARMA1 and Bcl10, but also by acting as a protease that cleaves multiple substrates to promote lymphocyte proliferation and survival via the NF-kappa B signalling pathway. Herein, we present the partial H-1, C-13 Ile/Val/Leu-Methyl resonance assignment of the monomeric apo form of the paracaspase-IgL(3) domain of human MALT1. Our results provide a solid ground for future elucidation of both the three-dimensional structure and the dynamics of MALT1, key for adequate development of inhibitors, and a thorough molecular understanding of its function(s).
|
|
| 7. |
- Köhler, Christian, et al.
(författare)
-
Backbone 1H, 13C, and 15N resonance assignments of the ligand binding domain of the human wildtype glucocorticoid receptor and the F602S mutant variant
- 2018
-
Ingår i: Biomolecular NMR Assignments. - : Springer Science and Business Media LLC. - 1874-2718 .- 1874-270X. ; 12:2, s. 263-268
-
Tidskriftsartikel (refereegranskat)abstract
- The glucocorticoid receptor (GR) is a nuclear hormone receptor that regulates key genes controlling development, metabolism, and the immune response. GR agonists are efficacious for treatment of inflammatory, allergic, and immunological disorders. Steroid hormone binding to the ligand-binding domain (LBD) of GR is known to change the structural and dynamical properties of the receptor, which in turn control its interactions with DNA and various co-regulators and drive the pharmacological response. Previous biophysical studies of the GR LBD have required the use of mutant forms to overcome issues with limited protein stability and high aggregation propensity. However, these mutant variants are known to also influence the functional response of the receptor. Here we report a successful protocol for protein expression, purification, and NMR characterization of the wildtype human GR LBD. We achieved chemical shift assignments for 90% of the LBD backbone resonances, with 216 out of 240 non-proline residues assigned in the 1H–15N TROSY spectrum. These advancements form the basis for future investigations of allosteric effects in GR signaling.
|
|
| 8. |
|
|
| 9. |
- Oktaviani, Nur Alia, et al.
(författare)
-
100% complete assignment of non-labile H-1, C-13, and N-15 signals for calcium-loaded calbindin D-9k P43G
- 2011
-
Ingår i: Biomolecular NMR Assignments. - : Springer Science and Business Media LLC. - 1874-2718 .- 1874-270X. ; 5:1, s. 79-84
-
Tidskriftsartikel (refereegranskat)abstract
- Here we present the 100% complete assignment chemical shift of non-labile H-1, N-15 and C-13 nuclei of Calbindin D-9k P43G. The assignment includes all non-exchangeable side chain nuclei, including ones that are rarely reported, such as LysN zeta as well as the termini. NMR experiments required to achieve truly complete assignments are discussed. To the best of our knowledge our assignments for Calbindin D-9k extend beyond previous studies reaching near-completeness (Vis et al. in Biochem 33:14858-14870, 1994; Yamazaki et al. in J Am Chem Soc 116:6464-6465, 1994; Yamazaki et al. in Biochem 32:5656-5669, 1993b).
|
|
| 10. |
|
|
| 11. |
- Saline, Maria, et al.
(författare)
-
Backbone resonance assignment of Staphylococcal Enterotoxin H.
- 2009
-
Ingår i: Biomolecular NMR assignments. - : Springer Science and Business Media LLC. - 1874-270X .- 1874-2718.
-
Tidskriftsartikel (refereegranskat)abstract
- The staphylococcal enterotoxin H (SEH; 217 aa, 25 kD) belongs to a family of superantigens that cause a massive immune response upon simultaneous binding to the T cell receptor (TCR) and the major histocompatibility complex class II. The SEH-TCR interaction is weak and amenable to studies using NMR methodology. Essentially, 2 mg of U{(2)H, (13)C,(15)N}-labeled SEH was used for the complete sequential backbone assignment of SEH at 900 MHz. The protein secondary structure inferred from the chemical shift index (C(alpha) and C(beta)) is in very good agreement with the secondary structure elements of the X-ray structure.
|
|
| 12. |
- Schnieders, R, et al.
(författare)
-
1H, 13C and 15N chemical shift assignment of the stem-loop 5a from the 5'-UTR of SARS-CoV-2
- 2021
-
Ingår i: Biomolecular NMR assignments. - : Springer Science and Business Media LLC. - 1874-270X .- 1874-2718. ; 15:1, s. 203-211
-
Tidskriftsartikel (refereegranskat)abstract
- The SARS-CoV-2 (SCoV-2) virus is the causative agent of the ongoing COVID-19 pandemic. It contains a positive sense single-stranded RNA genome and belongs to the genus of Betacoronaviruses. The 5′- and 3′-genomic ends of the 30 kb SCoV-2 genome are potential antiviral drug targets. Major parts of these sequences are highly conserved among Betacoronaviruses and contain cis-acting RNA elements that affect RNA translation and replication. The 31 nucleotide (nt) long highly conserved stem-loop 5a (SL5a) is located within the 5′-untranslated region (5′-UTR) important for viral replication. SL5a features a U-rich asymmetric bulge and is capped with a 5′-UUUCGU-3′ hexaloop, which is also found in stem-loop 5b (SL5b). We herein report the extensive 1H, 13C and 15N resonance assignment of SL5a as basis for in-depth structural studies by solution NMR spectroscopy.
|
|
| 13. |
- Schulte, T., et al.
(författare)
-
Assigned NMR backbone resonances of the ligand-binding region domain of the pneumococcal serine-rich repeat protein (PsrP-BR) reveal a rigid monomer in solution
- 2020
-
Ingår i: Biomolecular NMR Assignments. - : Springer. - 1874-2718 .- 1874-270X.
-
Tidskriftsartikel (refereegranskat)abstract
- The pneumococcal serine rich repeat protein (PsrP) is displayed on the surface of Streptococcus pneumoniae with a suggested role in colonization in the human upper respiratory tract. Full-length PsrP is a 4000 residue-long multi-domain protein comprising a positively charged functional binding region (BR) domain for interaction with keratin and extracellular DNA during pneumococcal adhesion and biofilm formation, respectively. The previously determined crystal structure of the BR domain revealed a flat compressed barrel comprising two sides with an extended β-sheet on one side, and another β-sheet that is distorted by loops and β-turns on the other side. Crystallographic B-factors indicated a relatively high mobility of loop regions that were hypothesized to be important for binding. Furthermore, the crystal structure revealed an inter-molecular β-sheet formed between edge strands of two symmetry-related molecules, which could promote bacterial aggregation during biofilm formation. Here we report the near complete 15N/13C/1H backbone resonance assignment of the BR domain of PsrP, revealing a secondary structure profile that is almost identical to the X-ray structure. Dynamic 15N-T1, T2 and NOE data suggest a monomeric and rigid structure of BR with disordered residues only at the N- and C-termini. The presented peak assignment will allow us to identify BR residues that are crucial for ligand binding.
|
|
| 14. |
- Ul Mushtaq, Ameeq, et al.
(författare)
-
Backbone chemical shift assignment and dynamics of the N-terminal domain of ClpB from Francisella tularensis type VI secretion system
- 2022
-
Ingår i: Biomolecular NMR Assignments. - : Springer. - 1874-2718 .- 1874-270X. ; 16, s. 75-79
-
Tidskriftsartikel (refereegranskat)abstract
- The Hsp100 family member ClpB is a protein disaggregase which solubilizes and reactivates stress-induced protein aggregates in cooperation with the DnaK/Hsp70 chaperone system. In the pathogenic bacterium Francisella tularensis, ClpB is involved in type VI secretion system (T6SS) disassembly through depolymerization of the IglA-IglB sheath. This leads to recycling and reassembly of T6SS components and this process is essential for the virulence of the bacterium. Here we report the backbone chemical shift assignments and 15N relaxation-based backbone dynamics of the N-terminal substrate-binding domain of ClpB (1-156).
|
|
| 15. |
- Wernersson, Sven, et al.
(författare)
-
Backbone H-1, C-13, and N-15 resonance assignments of BoMan26A, a -mannanase of the glycoside hydrolase family 26 from the human gut bacterium Bacteroides ovatus
- 2019
-
Ingår i: Biomolecular NMR Assignments. - : Springer Science and Business Media LLC. - 1874-2718 .- 1874-270X. ; 13:1, s. 213-218
-
Tidskriftsartikel (refereegranskat)abstract
- Bacteroides ovatus is a member of the human gut microbiota. The importance of this microbial consortium involves the degradation of complex dietary glycans mainly conferred by glycoside hydrolases. In this study we focus on one such catabolic glycoside hydrolase from B. ovatus. The enzyme, termed BoMan26A, is a -mannanase that takes part in the hydrolytic degradation of galactomannans. The crystal structure of BoMan26A has previously been determined to reveal a TIM-barrel like fold, but the relation between the protein structure and the mode of substrate processing has not yet been studied. Here we report residue-specific assignments for 95% of the 344 backbone amides of BoMan26A. The assignments form the basis for future studies of the relationship between substrate interactions and protein dynamics. In particular, the potential role of loops adjacent to glycan binding sites is of interest for such studies.
|
|
| 16. |
|
|
