{"title":"Solution-state NMR assignment and secondary structure propensity of the full length and minimalistic-truncated prefibrillar monomeric form of biofilm forming functional amyloid FapC from Pseudomonas aeruginosa","authors":"Chang-Hyeock Byeon, Pang C. Wang, In-Ja L. Byeon, Ümit Akbey","doi":"10.1007/s12104-023-10135-5","DOIUrl":"10.1007/s12104-023-10135-5","url":null,"abstract":"<div><p>Functional bacterial amyloids provide structural scaffolding to bacterial biofilms. In contrast to the pathological amyloids, they have a role in vivo and are tightly regulated. Their presence is essential to the integrity of the bacterial communities surviving in biofilms and may cause serious health complications. Targeting amyloids in biofilms could be a novel approach to prevent chronic infections. However, structural information is very scarce on them in both soluble monomeric and insoluble fibrillar forms, hindering our molecular understanding and strategies to fight biofilm related diseases. Here, we present solution-state NMR assignment of 250 amino acid long biofilm-forming functional-amyloid FapC from <i>Pseudomonas aeruginosa</i>. We studied full-length (FL) and shorter minimalistic-truncated (L2R3C) FapC constructs without the signal-sequence that is required for secretion. 91% and 100% backbone NH resonance assignments for FL and L2R3C constructs, respectively, indicate that soluble monomeric FapC is predominantly disordered, with sizeable secondary structural propensities mostly as PP2 helices, but also as α-helices and β-sheets highlighting hotspots for fibrillation initiation interface. A shorter construct showing almost identical NMR chemical shifts highlights the promise of utilizing it for more demanding solid-state NMR studies that require methods to alleviate signal redundancy due to almost identical repeat units. This study provides key NMR resonance assignments for future structural studies of soluble, pre-fibrillar and fibrillar forms of FapC.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"17 2","pages":"159 - 165"},"PeriodicalIF":0.9,"publicationDate":"2023-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9440635","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Solution NMR backbone assignment of the SASH1 SLy proteins associated disordered region (SPIDER)","authors":"Christopher M. Clements, Beat Vögeli, Yiqun G. Shellman, Morkos A. Henen","doi":"10.1007/s12104-023-10134-6","DOIUrl":"10.1007/s12104-023-10134-6","url":null,"abstract":"<div><p>SASH1 is a scaffold protein with context-dependent biological functions in cell adhesion, tumor metastasis, lung development, and pigmentation. As a member of the SLy protein family, it contains the conserved SLY, SH3, and SAM domains. The 19 kDa SLY domain harbors over 70% of the SASH1 variants associated with pigmentation disorders. However, its solution structure or dynamics have not been investigated yet, and its exact position in the sequence is not clearly defined. Based on the bioinformatic and experimental evidence, we propose renaming this region to the <u>S</u>Ly <u>P</u>roteins Assoc<u>i</u>ated <u>D</u>isorder<u>e</u>d <u>R</u>egion (SPIDER) and defining the exact position to be amino acids 400–554 of SASH1. We have previously identified a variant in this region linked to a pigmentation disorder, S519N. Here, we used a novel deuteration technique, a suite of TROSY-based 3D NMR experiments, and a high-quality HNN to obtain near complete solution backbone assignment of SASH1’s SPIDER. A comparison with the chemical shifts of non-variant (S519) SPIDER shows that the S519N substitution does not alter the free form solution structural propensities of SPIDER. This assignment is the first step to characterize the role of SPIDER in SASH1-mediated cellular functions and provides a model for the future study of sister SPIDER domains in the SLy protein family.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"17 1","pages":"151 - 157"},"PeriodicalIF":0.9,"publicationDate":"2023-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12104-023-10134-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4356446","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"1 H, 15 N, and 13 C backbone and side chain resonance assignments of the cold shock domain of the Arabidopsis thaliana glycine-rich protein AtGRP2","authors":"Karina C. Pougy, Gilberto Sachetto-Martins, Fabio C. L. Almeida, Anderson S. Pinheiro","doi":"10.1007/s12104-023-10133-7","DOIUrl":"10.1007/s12104-023-10133-7","url":null,"abstract":"<div><p>AtGRP2 (<i>Arabidopsis thaliana</i> glycine-rich protein 2) is a 19-kDa RNA-binding glycine-rich protein that regulates key processes in <i>A. thaliana</i>. AtGRP2 is a nucleo-cytoplasmic protein with preferential expression in developing tissues, such as meristems, carpels, anthers, and embryos. AtGRP2 knockdown leads to an early flowering phenotype. In addition, AtGRP2-silenced plants exhibit a reduced number of stamens and abnormal development of embryos and seeds, suggesting its involvement in plant development. AtGRP2 expression is highly induced by cold and abiotic stresses, such as high salinity. Moreover, AtGRP2 promotes double-stranded DNA/RNA denaturation, indicating its role as an RNA chaperone during cold acclimation. AtGRP2 is composed of an N-terminal cold shock domain (CSD) followed by a C-terminal flexible region containing two CCHC-type zinc fingers interspersed with glycine-rich sequences. Despite its functional relevance in flowering time regulation and cold adaptation, the molecular mechanisms employed by AtGRP2 are largely unknown. To date, there is no structural information regarding AtGRP2 in the literature. Here, we report the <sup>1</sup>H, <sup>15</sup>N, and <sup>13</sup>C backbone and side chain resonance assignments, as well as the chemical shift-derived secondary structure propensities, of the N-terminal cold shock domain of AtGRP2, encompassing residues 1–90. These data provide a framework for AtGRP2-CSD three-dimensional structure, dynamics, and RNA binding specificity investigation, which will shed light on its mechanism of action.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"17 1","pages":"143 - 149"},"PeriodicalIF":0.9,"publicationDate":"2023-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4222548","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Backbone and ILV side-chain methyl NMR resonance assignments of human Rev7/Rev3-RBM1 and Rev7/Rev3-RBM2 complexes","authors":"Gianluca A. Arianna, Dane H. Geddes-Buehre, Dmitry M. Korzhnev","doi":"10.1007/s12104-023-10128-4","DOIUrl":"10.1007/s12104-023-10128-4","url":null,"abstract":"<div><p>Rev7 is a versatile HORMA (Hop1, Rev7, Mad2) family adaptor protein with multiple roles in mitotic regulation and DNA damage response, and an essential accessory subunit of the translesion synthesis (TLS) DNA polymerase Polζ employed in replication of damaged DNA. Within Polζ, the two copies of Rev7 interact with the two Rev7-bonding motifs (RBM1 and RBM2) of the catalytic subunit Rev3 by a mechanism characteristic of HORMA proteins whereby the “safety-belt” loop of Rev7 closes on the top of the ligand. Here we report the nearly complete backbone and Ile, Val, Leu side-chain methyl NMR resonance assignments of the 27 kDa human Rev7/Rev3-RBM1 and Rev7/Rev3-RBM2 complexes (BMRB deposition numbers 51651 and 51652) that will facilitate future NMR studies of Rev7 dynamics and interactions.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"17 1","pages":"107 - 114"},"PeriodicalIF":0.9,"publicationDate":"2023-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12104-023-10128-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4097338","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Chemical shift assignments of retinal guanylyl cyclase activating protein 5 (GCAP5) with a mutation (R22A) that abolishes dimerization and enhances cyclase activation","authors":"Diana Cudia, Effibe O. Ahoulou, James B. Ames","doi":"10.1007/s12104-023-10129-3","DOIUrl":"10.1007/s12104-023-10129-3","url":null,"abstract":"<div><p>Retinal membrane guanylyl cyclases (RetGCs) in vertebrate rod and cone photoreceptors are activated by a family of neuronal Ca<sup>2+</sup> sensor proteins called guanylyl cyclase activating proteins (GCAP1-7). GCAP5 from zebrafish photoreceptors binds to RetGC and confers Ca<sup>2+</sup>/Fe<sup>2+</sup>-dependent regulation of RetGC enzymatic activity that promotes the recovery phase of visual phototransduction. We report NMR chemical shift assignments of GCAP5 with a R22A mutation (called GCAP5<sup>R22A</sup>) that abolishes protein dimerization and activates RetGC with 3-fold higher activity than that of wild type GCAP5 (BMRB No. 51,783).</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"17 1","pages":"115 - 119"},"PeriodicalIF":0.9,"publicationDate":"2023-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12104-023-10129-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4098512","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"1H, 13C, 15N backbone chemical shift assignments of the extended ARID domain in human AT-rich interactive domain protein 5a (Arid5a)","authors":"Julian von Ehr, Sophie Marianne Korn, Lena Weiß, Andreas Schlundt","doi":"10.1007/s12104-023-10130-w","DOIUrl":"10.1007/s12104-023-10130-w","url":null,"abstract":"<div><p>The family of AT-rich interactive domain (ARID) containing proteins -<i>Arids</i>- contains 15 members that have almost exclusively been described as DNA-binding proteins. Interestingly, a decade ago the family member <i>Arid5a</i> was found to bind and stabilize mRNAs of immune system key players and thereby account for driving inflammatory and autoimmune diseases. How exactly binding to DNA and RNA is coordinated by the <i>Arid5a</i> ARID domain remains unknown, mainly due to the lack of atom-resolved information on nucleic acid-binding. This in particular applies to the protein’s ARID domain, despite the comfortable size of its core unit for NMR-based investigations. Furthermore, the core domain of ARID domains is found to be extended by functionally relevant, often flexible stretches, but whether such elongations are present and crucial for the versatile <i>Arid5a</i> functions is unknown. We here provide a near-complete NMR backbone resonance assignment of the <i>Arid5a</i> ARID domain with N- and C-terminal extensions, which serves as a basis for further studies of its nucleic acid-binding preferences and targeted inhibition by means of NMR. Our data thus significantly contribute to unravelling mechanisms of <i>Arid5a</i>-mediated gene regulation and diseases.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"17 1","pages":"121 - 127"},"PeriodicalIF":0.9,"publicationDate":"2023-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12104-023-10130-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4440021","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"NMR resonance assignment of a fibroblast growth factor 8 splicing isoform b","authors":"Bruno Hargittay, Konstantin S. Mineev, Christian Richter, Sridhar Sreeramulu, Hendrik R.A. Jonker, Krishna Saxena, Harald Schwalbe","doi":"10.1007/s12104-023-10132-8","DOIUrl":"10.1007/s12104-023-10132-8","url":null,"abstract":"<div><p>The splicing isoform b of human fibroblast growth factor 8 (FGF8b) is an important regulator of brain embryonic development. Here, we report the almost complete NMR chemical shift assignment of the backbone and aliphatic side chains of FGF8b. Obtained chemical shifts are in good agreement with the previously reported X-ray data, excluding the N-terminal gN helix, which apparently forms only in complex with the receptor. The reported data provide an NMR starting point for the investigation of FGF8b interaction with its receptors and with potential drugs or inhibitors.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"17 1","pages":"135 - 142"},"PeriodicalIF":0.9,"publicationDate":"2023-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12104-023-10132-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5589130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Resonance assignments of the microtubule-binding domain of the microtubule-associated protein 7 (MAP7)","authors":"Agnes Adler, Lenette F. Kjaer, J. Wouter Beugelink, Marc Baldus, Hugo van Ingen","doi":"10.1007/s12104-023-10124-8","DOIUrl":"10.1007/s12104-023-10124-8","url":null,"abstract":"<div><p>The microtubule-associated protein 7 (MAP7) is a protein involved in cargo transport along microtubules (MTs) by interacting with kinesin-1 through the C-terminal kinesin-binding domain. Moreover, the protein is reported to stabilize MT, thereby playing a key role in axonal branch development. An important element for this latter function is the 112 amino-acid long N-terminal microtubule-binding domain (MTBD) of MAP7. Here we report NMR backbone and side-chain assignments that suggest a primarily alpha-helical secondary fold of this MTBD in solution. The MTBD contains a central long α-helical segment that includes a short four-residue ‘hinge’ sequence with decreased helicity and increased flexibility. Our data represent a first step towards analysing the complex interaction of MAP7 with MTs at an atomic level via NMR spectroscopy.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"17 1","pages":"83 - 88"},"PeriodicalIF":0.9,"publicationDate":"2023-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12104-023-10124-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4997779","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Chemical shift assignments of calmodulin bound to a cytosolic domain of GluN2A (residues 1004–1024) from the NMDA receptor","authors":"Aritra Bej, James B. Ames","doi":"10.1007/s12104-023-10125-7","DOIUrl":"10.1007/s12104-023-10125-7","url":null,"abstract":"<div><p>N-methyl-D-aspartate receptors (NMDARs) consist of glycine-binding GluN1 and glutamate-binding GluN2 subunits that form tetrameric ion channels. NMDARs in the neuronal post-synaptic membrane are important for controlling neuroplasticity and synaptic transmission in the brain. Calmodulin (CaM) binds to the cytosolic C0 domains of both GluN1 (residues 841–865) and GluN2 (residues 1004–1024) that may play a role in the Ca<sup>2+</sup>-dependent desensitization of NMDAR channels. Mutations that disrupt Ca<sup>2+</sup>-dependent desensitization of NMDARs are linked to Alzheimer’s disease, depression, stroke, epilepsy, and schizophrenia. NMR chemical shift assignments are reported here for Ca<sup>2+</sup>-saturated CaM bound to the GluN2A C0 domain of NMDAR (BMRB no. 51821).</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"17 1","pages":"89 - 93"},"PeriodicalIF":0.9,"publicationDate":"2023-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12104-023-10125-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4606241","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"1H, 15N, 13C backbone and Cβ resonance assignments for UBQLN1 UBA and UBAA domains","authors":"Gwen R. Buel, Xiang Chen, Olumide Kayode, Anthony Cruz, Kylie J. Walters","doi":"10.1007/s12104-023-10127-5","DOIUrl":"10.1007/s12104-023-10127-5","url":null,"abstract":"<div><p>UBQLN1 functions in autophagy and proteasome-mediated protein degradation. It contains an N-terminal ubiquitin-like domain (UBL), a C-terminal ubiquitin-associated domain (UBA), and a flexible central region which functions as a chaperone to prevent protein aggregation. Here, we report the <sup>1</sup>H, <sup>15</sup>N, and <sup>13</sup>C resonance assignments for the backbone (<sup>N</sup>H, N, C’, Cα, and Hα) and sidechain Cβ atoms of the UBQLN1 UBA and an N-terminally adjacent segment called the UBA-adjacent domain (UBAA). We find a subset of the resonances corresponding to the UBAA to have concentration-dependent chemical shifts, likely due to self-association. We also find the backbone amide nitrogen of T572 to be shifted upfield relative to the average value for a threonine amide nitrogen, a phenomenon likely caused by T572 Hγ1 engagement in a hydrogen bond with adjacent backbone carbonyl atoms. The assignments described in this manuscript can be used to study the protein dynamics of the UBQLN1 UBA and UBAA as well as the interaction of these domains with other proteins.</p></div>","PeriodicalId":492,"journal":{"name":"Biomolecular NMR Assignments","volume":"17 1","pages":"101 - 106"},"PeriodicalIF":0.9,"publicationDate":"2023-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s12104-023-10127-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4238043","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}