The C-terminal transactivation domain of MITF interacts promiscuously with co-activator CBP/p300.

The microphthalmia-associated transcription factor (MITF) is one of four closely related members of the MiT/TFE family (TFEB, TFE3, TFEC) that regulate a wide range of cellular processes. MITF is a key regulator of melanocyte-associated genes, and essential to proper development of the melanocyte cell lineage. Abnormal MITF activity can contribute to the onset of several diseases including melanoma, where MITF is an amplified oncogene. To enhance transcription, MITF recruits the co-activator CREB-binding protein (CBP) and its homolog p300 to gene promoters, however the molecular determinants of their interaction are not yet fully understood. Here, we characterize the interactions between the C-terminal MITF transactivation domain and CBP/p300. Using NMR spectroscopy, protein pulldown assays, and isothermal titration calorimetry we determine the C-terminal region of MITF is intrinsically disordered and binds with high-affinity to both TAZ1 and TAZ2 of CBP/p300. Mutagenesis studies revealed two conserved motifs within MITF that are necessary for TAZ2 binding and critical for MITF-dependent transcription of a reporter gene. Finally, we observe the transactivation potential of the MITF C-terminal region is reliant on the N-terminal transactivation domain for function. Taken together, our study helps elucidate the molecular details of how MITF interacts with CBP/p300 through multiple redundant interactions that lend insight into MITF function in melanocytes and melanoma.

Structural basis of CBP/p300 recruitment by the microphthalmia-associated transcription factor.

The microphthalmia-associated transcription factor (MITF) is a master regulator of the melanocyte cell lineage. Aberrant MITF activity can lead to multiple malignancies including skin cancer, where it modulates the progression and invasiveness of melanoma. MITF-regulated gene expression requires recruitment of the transcriptional co-regulator CBP/p300, but details of this process are not fully defined. In this study, we investigate the structural and functional interaction between the MITF N-terminal transactivation domain (MITFTAD) and CBP/p300. Using pulldown assays and nuclear magnetic resonance spectroscopy we determined that MITFTAD is intrinsically disordered and binds to the TAZ1 and TAZ2 domains of CBP/p300 with moderate affinity. The solution-state structure of the MITFTAD:TAZ2 complex reveals that MITF interacts with a hydrophobic surface of TAZ2, while remaining somewhat dynamic. Peptide array and mutagenesis experiments determined that an acidic motif is integral to the MITFTAD:TAZ2 interaction and is necessary for transcriptional activity of MITF. Peptides that bind to the same surface of TAZ2 as MITFTAD, such as the adenoviral protein E1A, are capable of displacing MITF from TAZ2 and inhibiting transactivation. These findings provide insight into co-activator recruitment by MITF that are fundamental to our understanding of MITF targeted gene regulation and melanoma biology.

Qualitative and Quantitative Characterization of Protein-Carbohydrate Interactions by NMR Spectroscopy.

Solution-state nuclear magnetic resonance (NMR) spectroscopy can be used to monitor protein-carbohydrate interactions. Two-dimensional 1H-15N heteronuclear single quantum coherence (HSQC)-based techniques described in this chapter can be used quickly and effectively to screen a set of possible carbohydrate-binding partners, to quantify the dissociation constant (Kd) of any identified interactions, and to the map the carbohydrate-binding site on the structure of a protein. Here, we describe the titration of a family 32 carbohydrate-binding module from Clostridium perfringens (CpCBM32) with the monosaccharide N-acetylgalactosamine (GalNAc), in which we calculate the apparent dissociation of the interaction and map the GalNAc binding site onto the structure of CpCBM32. This approach can be applied to other CBM- and protein-ligand systems.

ß-Catenin interacts with the TAZ1 and TAZ2 domains of CBP/p300 to activate gene transcription.

The transcriptional co-regulator ß-catenin is a critical member of the canonical Wnt signaling pathway, which plays an important role in regulating cell fate. Deregulation of the Wnt/ß-catenin pathway is characteristic in the development of major types of cancer, where accumulation of ß-catenin promotes cancer cell proliferation and renewal. ß-catenin gene expression is facilitated through recruitment of co-activators such as histone acetyltransferases CBP/p300; however, the mechanism of their interaction is not fully understood. Here we investigate the interaction between the C-terminal transactivation domain of ß-catenin and CBP/p300. Using a combination of pulldown assays, isothermal titration calorimetry, and nuclear resonance spectroscopy we determine the disordered C-terminal region of ß-catenin binds promiscuously to the TAZ1 and TAZ2 domains of CBP/p300. We then map the interaction site of the C-terminal ß-catenin transactivation domain onto TAZ1 and TAZ2 using chemical-shift perturbation studies. Luciferase-based gene reporter assays indicate Asp750-Leu781 is critical to ß-catenin gene activation, and mutagenesis revealed that acidic and hydrophobic residues within this region are necessary to maintain TAZ1 binding. These results outline a mechanism of Wnt/ß-catenin gene regulation that underlies cell development and provides a framework to develop methods to block ß-catenin dependent signaling.

PML and PML-like exonucleases restrict retrotransposons in jawed vertebrates.

We have uncovered a role for the promyelocytic leukemia (PML) gene and novel PML-like DEDDh exonucleases in the maintenance of genome stability through the restriction of LINE-1 (L1) retrotransposition in jawed vertebrates. Although the mammalian PML protein forms nuclear bodies, we found that the spotted gar PML ortholog and related proteins in fish function as cytoplasmic DEDDh exonucleases. In contrast, PML proteins from amniote species localized both to the cytoplasm and formed nuclear bodies. We also identified the PML-like exon 9 (Plex9) genes in teleost fishes that encode exonucleases. Plex9 proteins resemble TREX1 but are unique from the TREX family and share homology to gar PML. We also characterized the molecular evolution of TREX1 and the first non-mammalian TREX1 homologs in axolotl. In an example of convergent evolution and akin to TREX1, gar PML and zebrafish Plex9 proteins suppressed L1 retrotransposition and could complement TREX1 knockout in mammalian cells. Following export to the cytoplasm, the human PML-I isoform also restricted L1 through its conserved C-terminus by enhancing ORF1p degradation through the ubiquitin-proteasome system. Thus, PML first emerged as a cytoplasmic suppressor of retroelements, and this function is retained in amniotes despite its new role in the assembly of nuclear bodies.

Characterization of the structure and self-assembly of two distinct class IB hydrophobins.

Hydrophobins are small proteins secreted by fungi that accumulate at interfaces, modify surface hydrophobicity, and self-assemble into large amyloid-like structures. These unusual properties make hydrophobins an attractive target for commercial applications as emulsifiers and surface modifying agents. Hydrophobins have diverse sequences and tertiary structures, complicating attempts to characterize how they function. Here we describe the atomic resolution structure of the unusual hydrophobin SLH4 (86 aa, 8.4 kDa) and compare its function to another hydrophobin, SC16 (99 aa, 10.2 kDa). Despite containing only one charged residue, SLH4 has a similar structure to SC16 yet has strikingly different rodlet morphology, propensity to self-assemble, and preferred assembly conditions. Secondary structure analysis of both SC16 and SLH4 suggest that during rodlet formation residues in the first intercysteine loop undergo conformational changes. This work outlines a representative structure for class IB hydrophobins and illustrates how hydrophobin surface properties govern self-assembly, which provides context to rationally select hydrophobins for applications as surface modifiers. KEY POINTS: • The atomic-resolution structure of the hydrophobin SLH4 was determined using nuclear magnetic resonance spectroscopy. • The structure of SLH4 outlines a representative structure for class IB hydrophobins. • The assembly characteristics of SLH4 and SC16 are distinct, outlining how surface properties of hydrophobins influence their function.

Bactericidal Activity of Carvacrol against Streptococcus pyogenes Involves Alteration of Membrane Fluidity and Integrity through Interaction with Membrane Phospholipids.

BACKGROUND: Carvacrol, a mono-terpenoid phenol found in herbs, such as oregano and thyme, has excellent antibacterial properties against Streptococcus pyogenes. However, its mechanism of bactericidal activity on S. pyogenes has not been elucidated. OBJECTIVES: This study investigated the bactericidal mechanism of carvacrol using three strains of S. pyogenes. METHODS: Flow cytometry (FCM) experiments were conducted to determine carvacrol's membrane permeabilization and cytoplasmic membrane depolarization activities. Protoplasts of S. pyogenes were used to investigate carvacrol's effects on the membrane, followed by gel electrophoresis. The carvacrol-treated protoplasts were examined by transmission electron microscopy (TEM) to observe ultrastructural morphological changes. The fluidity of the cell membrane was measured by steady-state fluorescence anisotropy. Thin-layer chromatographic (TLC) profiling was conducted to study the affinity of carvacrol for membrane phospholipids. RESULTS: Increased membrane permeability and decreased membrane potential from FCM and electron microscopy observations revealed that carvacrol killed the bacteria primarily by disrupting membrane integrity, leading to whole-cell lysis. Ultra-structural morphological changes in the membrane induced by carvacrol over a short period were confirmed using the S. pyogenes protoplast and membrane isolate models in vitro. In addition, changes in the other biophysical properties of the bacterial membrane, including concentration- and time-dependent increased fluidity, were observed. TLC experiments showed that carvacrol preferentially interacts with membrane phosphatidylglycerol (P.G.), phosphatidylethanolamine (P.E.), and cardiolipins (CL). CONCLUSIONS: Carvacrol exhibited rapid bactericidal action against S. pyogenes by disrupting the bacterial membrane and increasing permeability, possibly due to affinity with specific membrane phospholipids, such as P.E., P.G., and CL. Therefore, the bactericidal concentration of carvacrol (250 µg/mL) could be used to develop safe and efficacious natural health products for managing streptococcal pharyngitis or therapeutic applications.

The N-terminal tail of the hydrophobin SC16 is not required for rodlet formation.

Hydrophobins are small proteins that are secreted by fungi, accumulate at interfaces, modify surface hydrophobicity, and self-assemble into large amyloid-like structures. These unusual properties make hydrophobins an attractive target for commercial applications as green emulsifiers and surface modifying agents. Hydrophobins have diverse sequences and tertiary structures, and depending on the hydrophobin, different regions of their structure have been proposed to be required for self-assembly. To provide insight into the assembly process, we determined the first crystal structure of a class I hydrophobin, SC16. Based on the crystal structure, we identified a putative intermolecular contact that may be important for rodlet assembly and was formed in part by the N-terminal tail of SC16. Surprisingly, removal of the N-terminal tail did not influence the self-assembly kinetics of SC16 or the morphology of its rodlets. These results suggest that other regions of this hydrophobin class are required for rodlet formation and indicate that the N-terminal tail of SC16 is amenable to modification so that functionalized hydrophobin assemblies can be created.

Microbial rhodoquinone biosynthesis proceeds via an atypical RquA-catalyzed amino transfer from S-adenosyl-L-methionine to ubiquinone.

Rhodoquinone (RQ) is a close analogue of ubiquinone (UQ) that confers diverse bacterial and eukaryotic taxa the ability to utilize fumarate as an electron acceptor in hypoxic conditions. The RquA protein, identified in a Rhodospirillum rubrum RQ-deficient mutant, has been shown to be required for RQ biosynthesis in bacteria. In this report, we demonstrate that RquA, homologous to SAM-dependent methyltransferases, is necessary and sufficient to catalyze RQ biosynthesis from UQ in vitro. Remarkably, we show that RquA uses SAM as the amino group donor in a substitution reaction that converts UQ to RQ. In contrast to known aminotransferases, RquA does not use pyridoxal 5'-phosphate (PLP) as a coenzyme, but requires the presence of Mn2+ as a cofactor. As these findings reveal, RquA provides an example of a non-canonical SAM-dependent enzyme that does not catalyze methyl transfer, instead it uses SAM in an atypical amino transfer mechanism.

Expression, purification, and refolding of diverse class IB hydrophobins.

Hydrophobins are low molecular weight proteins secreted by fungi that are extremely surface-active and able to self-assemble into larger structures. Due to their unusual biochemical properties, hydrophobins are an attractive target for commercial applications such as drug emulsification and surface modification. When produced in E. coli, hydrophobins are often not soluble and need to be refolded. In this work we use SHuffle T7 Express E. coli coupled with glutathione redox buffers to produce and refold four distinct class IB hydrophobins that originate from Phanerochaete carnosa (PC1), Wallemia ichthyophaga (WI1), Serpula lacrymans (SL1), and Schizophyllum commune (SC16). Proper refolding and function of these purified hydrophobins was confirmed using nuclear magnetic resonance spectroscopy and thioflavin T assays. These results indicate that class IB hydrophobins can be consistently produced and purified from E. coli, aiding future structural and biochemical studies that require highly pure hydrophobins.

Rhodoquinone in bacteria and animals: Two distinct pathways for biosynthesis of this key electron transporter used in anaerobic bioenergetics.

The terpenoid benzoquinone, rhodoquinone (RQ), is essential to the bioenergetics of many organisms that survive in low oxygen environments. RQ biosynthesis and its regulation has potential as a novel target for anti-microbial and anti-parasitic drug development. Recent work has uncovered two distinct pathways for RQ biosynthesis which have evolved independently. The first pathway is used by bacteria, such as Rhodospirillum rubrum, and some protists that possess the rquA gene. These species derive their RQ directly from ubiquinone (UQ), the essential electron transporter used in the aerobic respiratory chain. The second pathway is used in animals, such as Caenorhabditis elegans and parasitic helminths, and requires 3-hydroxyanthranilic acid (3-HAA) as a precursor, which is derived from tryptophan through the kynurenine pathway. A COQ-2 isoform, which is unique to these species, facilitates prenylation of the 3-HAA precursor. After prenylation, the arylamine ring is further modified to form RQ using several enzymes common to the UQ biosynthetic pathway. In addition to current knowledge of RQ biosynthesis, we review the phylogenetic distribution of RQ and its function in anaerobic electron transport chains in bacteria and animals. Finally, we discuss key steps in RQ biosynthesis that offer potential as drug targets to treat microbial and parasitic infections, which are rising global health concerns.

Structural insights into TAZ2 domain-mediated CBP/p300 recruitment by transactivation domain 1 of the lymphopoietic transcription factor E2A.

The E-protein transcription factors guide immune cell differentiation, with E12 and E47 (hereafter called E2A) being essential for B-cell specification and maturation. E2A and the oncogenic chimera E2A-PBX1 contain three transactivation domains (ADs), with AD1 and AD2 having redundant, independent, and cooperative functions in a cell-dependent manner. AD1 and AD2 both mediate their functions by binding to the KIX domain of the histone acetyltransferase paralogues CREB-binding protein (CBP) and E1A-binding protein P300 (p300). This interaction is necessary for B-cell maturation and oncogenesis by E2A-PBX1 and occurs through conserved ΦXXΦΦ motifs (with Φ denoting a hydrophobic amino acid) in AD1 and AD2. However, disruption of this interaction via mutation of the KIX domain in CBP/p300 does not completely abrogate binding of E2A and E2A-PBX1. Here, we determined that E2A-AD1 and E2A-AD2 also interact with the TAZ2 domain of CBP/p300. Characterization of the TAZ2:E2A-AD1(1-37) complex indicated that E2A-AD1 adopts an α-helical structure and uses its ΦXXΦΦ motif to bind TAZ2. Whereas this region overlapped with the KIX recognition region, key KIX-interacting E2A-AD1 residues were exposed, suggesting that E2A-AD1 could simultaneously bind both the KIX and TAZ2 domains. However, we did not detect a ternary complex involving E2A-AD1, KIX, and TAZ2 and found that E2A containing both intact AD1 and AD2 is required to bind to CBP/p300. Our findings highlight the structural plasticity and promiscuity of E2A-AD1 and suggest that E2A binds both the TAZ2 and KIX domains of CBP/p300 through AD1 and AD2.

Periodicity in Structure, Bonding, and Reactivity for p-Block Complexes of a Geometry Constraining Triamide Ligand.

The use of pincer ligands to access non-VSEPR geometries at main-group centers is an emerging strategy for eliciting new stoichiometric and catalytic reactivity. As part of this effort, several different tridentate trianionic substituents have to date been employed at a range of different central elements, providing a patchwork dataset that precludes rigorous structure-function correlation. An analysis of periodic trends in structure (solid, solution, and computation), bonding, and reactivity based on systematic variation of the central element (P, As, Sb, or Bi) with retention of a single tridentate triamide substituent is reported herein. In this homologous series, the central element can adopt either a bent or planar geometry. The tendency to adopt planar geometries increases descending the group with the phosphorus triamide (1) and its arsenic congener (2) exhibiting bent conformations, and the antimony (3) and bismuth (4) analogues exhibiting a predominantly planar structure in solution. This trend has been rationalized using an energy decomposition analysis. A rare phase-dependent dynamic covalent dimerization was observed for 3 and the associated thermodynamic parameters were established quantitatively. Planar geometries were found to engender lower LUMO energies and smaller band gaps than bent ones, resulting in different reactivity patterns. These results provide a benchmark dataset to guide further research in this rapidly emerging area.

Conserved structural features anchor biofilm-associated RTX-adhesins to the outer membrane of bacteria.

Repeats-in-toxin (RTX) adhesins are present in many Gram-negative bacteria to facilitate biofilm formation. Previously, we reported that the 1.5-MDa RTX adhesin (MpIBP) from the Antarctic bacterium, Marinomonas primoryensis, is tethered to the bacterial cell surface via its N-terminal Region I (RI). Here, we show the detailed structural features of RI. It has an N-terminal periplasmic retention domain (RIN), a central domain (RIM) that can insert into the ß-barrel of an outer-membrane pore protein during MpIBP secretion, and three extracellular domains at its C terminus (RIC) that transition the protein into the extender region (RII). RIN has a novel ß-sandwich fold with a similar shape to ßγ-crystallins and tryptophan RNA attenuation proteins. Because RIM undergoes fast and extensive degradation in vitro, its narrow cylindrical shape was rapidly measured by small-angle X-ray scattering before proteolysis could occur. The crystal structure of RIC comprises three tandem ß-sandwich domains similar to those in RII, but increasing in their hydrophobicity with proximity to the outer membrane. In addition, the key Ca2+ ion that rigidifies the linkers between RII domains is not present between the first two of these RIC domains. This more flexible RI linker near the cell surface can act as a 'pivot' to help the 0.6-µm-long MpIBP sweep over larger volumes to find its binding partners. Since the physical features of RI are well conserved in the RTX adhesins of many Gram-negative bacteria, our detailed structural and bioinformatic analyses serve as a model for investigating the surface retention of biofilm-forming bacteria, including human pathogens.

Properties of a family 56 carbohydrate-binding module and its role in the recognition and hydrolysis of ß-1,3-glucan.

BH0236 from Bacillus halodurans is a multimodular ß-1,3-glucanase comprising an N-terminal family 81 glycoside hydrolase catalytic module, an internal family 6 carbohydrate-binding module (CBM) that binds the nonreducing end of ß-1,3-glucan chains, and an uncharacterized C-terminal module classified into CBM family 56. Here, we determined that this latter CBM, BhCBM56, bound the soluble ß-1,3-glucan laminarin with a dissociation constant (Kd ) of ∼26 µm and displayed higher affinity for insoluble ß-1,3-glucans with Kd values of ∼2-10 µm but lacked affinity for ß-1,3-glucooligosaccharides. The X-ray crystal structure of BhCBM56 and NMR-derived chemical shift mapping of the binding site revealed a ß-sandwich fold, with the face of one ß-sheet possessing the ß-1,3-glucan-binding surface. On the basis of the functional and structural properties of BhCBM56, we propose that it binds a quaternary polysaccharide structure, most likely the triple helix adopted by polymerized ß-1,3-glucans. Consistent with the BhCBM56 and BhCBM6/56 binding profiles, deletion of the CBM56 from BH0236 decreased activity of the enzyme on the insoluble ß-1,3-glucan curdlan but not on soluble laminarin; additional deletion of the CBM6 also did not affect laminarin degradation but further decreased curdlan hydrolysis. The pseudo-atomic solution structure of BH0236 determined by small-angle X-ray scattering revealed structural insights into the nature of avid binding by the BhCBM6/56 pair and how the orientation of the active site in the catalytic module factors into recognition and degradation of ß-1,3-glucans. Our findings reinforce the notion that catalytic modules and their cognate CBMs have complementary specificities, including targeting of polysaccharide quaternary structure.

Structure of a 1.5-MDa adhesin that binds its Antarctic bacterium to diatoms and ice.

Bacterial adhesins are modular cell-surface proteins that mediate adherence to other cells, surfaces, and ligands. The Antarctic bacterium Marinomonas primoryensis uses a 1.5-MDa adhesin comprising over 130 domains to position it on ice at the top of the water column for better access to oxygen and nutrients. We have reconstructed this 0.6-µm-long adhesin using a "dissect and build" structural biology approach and have established complementary roles for its five distinct regions. Domains in region I (RI) tether the adhesin to the type I secretion machinery in the periplasm of the bacterium and pass it through the outer membrane. RII comprises ~120 identical immunoglobulin-like ß-sandwich domains that rigidify on binding Ca2+ to project the adhesion regions RIII and RIV into the medium. RIII contains ligand-binding domains that join diatoms and bacteria together in a mixed-species community on the underside of sea ice where incident light is maximal. RIV is the ice-binding domain, and the terminal RV domain contains several "repeats-in-toxin" motifs and a noncleavable signal sequence that target proteins for export via the type I secretion system. Similar structural architecture is present in the adhesins of many pathogenic bacteria and provides a guide to finding and blocking binding domains to weaken infectivity.

Peptide backbone circularization enhances antifreeze protein thermostability.

Antifreeze proteins (AFPs) are a class of ice-binding proteins that promote survival of a variety of cold-adapted organisms by decreasing the freezing temperature of bodily fluids. A growing number of biomedical, agricultural, and commercial products, such as organs, foods, and industrial fluids, have benefited from the ability of AFPs to control ice crystal growth and prevent ice recrystallization at subzero temperatures. One limitation of AFP use in these latter contexts is their tendency to denature and irreversibly lose activity at the elevated temperatures of certain industrial processing or large-scale AFP production. Using the small, thermolabile type III AFP as a model system, we demonstrate that AFP thermostability is dramatically enhanced via split intein-mediated N- and C-terminal end ligation. To engineer this circular protein, computational modeling and molecular dynamics simulations were applied to identify an extein sequence that would fill the 20-Å gap separating the free ends of the AFP, yet impose little impact on the structure and entropic properties of its ice-binding surface. The top candidate was then expressed in bacteria, and the circularized protein was isolated from the intein domains by ice-affinity purification. This circularized AFP induced bipyramidal ice crystals during ice growth in the hysteresis gap and retained 40% of this activity even after incubation at 100°C for 30 min. NMR analysis implicated enhanced thermostability or refolding capacity of this protein compared to the noncyclized wild-type AFP. These studies support protein backbone circularization as a means to expand the thermostability and practical applications of AFPs.

Preserved Transmembrane Segment Topology, Structure, and Dynamics in Disparate Micellar Environments.

Detergent micelles are frequently employed as membrane mimetics for solution-state membrane protein nuclear magnetic resonance spectroscopy. Here we compare topology, structure, ps-ns time-scale dynamics, and hydrodynamics of a model protein with one transmembrane (TM) segment (residues 1-55 of the apelin receptor, APJ, a G-protein-coupled receptor) in three distinct, commonly used micellar environments. In each environment, two solvent-protected helical segments connected by a solvent-exposed kink were observed. The break in helical character at the kink was maintained in a helix-stabilizing fluorinated alcohol environment, implying that this structural feature is inherent. Molecular dynamics simulations also substantiate favorable self-assembly of compact protein-micelle complexes with a more dynamic, solvent-exposed kink. Despite the observed similarity in TM segment behavior, micelle-dependent differences were clear in the structure, dynamics, and compactness of the 30-residue, extramembrane N-terminal tail of the protein. This would affect intermolecular interactions and, correspondingly, the functional state of the membrane protein.

Characterization of a Basidiomycota hydrophobin reveals the structural basis for a high-similarity Class I subdivision.

Class I hydrophobins are functional amyloids secreted by fungi. They self-assemble into organized films at interfaces producing structures that include cellular adhesion points and hydrophobic coatings. Here, we present the first structure and solution properties of a unique Class I protein sequence of Basidiomycota origin: the Schizophyllum commune hydrophobin SC16 (hyd1). While the core ß-barrel structure and disulphide bridging characteristic of the hydrophobin family are conserved, its surface properties and secondary structure elements are reminiscent of both Class I and II hydrophobins. Sequence analyses of hydrophobins from 215 fungal species suggest this structure is largely applicable to a high-identity Basidiomycota Class I subdivision (IB). To validate this prediction, structural analysis of a comparatively distinct Class IB sequence from a different fungal order, namely the Phanerochaete carnosa PcaHyd1, indicates secondary structure properties similar to that of SC16. Together, these results form an experimental basis for a high-identity Class I subdivision and contribute to our understanding of functional amyloid formation.

Characterization of Protein-Carbohydrate Interactions by NMR Spectroscopy.

Solution-state nuclear magnetic resonance (NMR) spectroscopy can be used to monitor protein-carbohydrate interactions. Two-dimensional 1H-15N heteronuclear single quantum coherence (HSQC)-based techniques described in this chapter can be used quickly and effectively to screen a set of possible carbohydrate binding partners, to quantify the dissociation constant (K d) of any identified interactions, and to map the carbohydrate binding site on the structure of the protein. Here, we describe the titration of a family 32 carbohydrate binding module from Clostridium perfringens (CpCBM32) with the monosaccharide N-acetylgalactosamine (GalNAc), in which we calculate the apparent dissociation of the interaction, and map the GalNAc binding site onto the structure of CpCBM32.