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1.
Int J Mol Sci ; 23(4)2022 Feb 09.
Article in English | MEDLINE | ID: mdl-35216047

ABSTRACT

Hundreds of millions of people around the world have been affected by Type 2 diabetes (T2D) which is a metabolic disorder. Clinical research has revealed T2D as a possible risk factor for Alzheimer's disease (AD) development (and vice versa). Amyloid-ß (Aß) and human islet amyloid polypeptide are the main pathological species in AD and T2D, respectively. However, the mechanisms by which these two amyloidogenic peptides co-aggregate are largely uninvestigated. Herein, for the first time, we present the cross-seeding between Amylin1-37 and Aß40 considering the particular effect of the histidine tautomerism at atomic resolution applying the all-atom molecular dynamics (MD) simulations for heterodimeric complexes. The results via random seed MD simulations indicated that the Aß40(δδδ) isomer in cross-talking with Islet(ε) and Islet(δ) isomers could retain or increase the ß-sheet content in its structure that may make it more prone to further aggregation and exhibit higher toxicity. The other tautomeric isomers which initially did not have a ß-sheet structure in their monomeric forms did not show any generated ß-sheet, except for one seed of the Islet(ε) and Aß40(εεε) heterodimers complex that displayed a small amount of formed ß-sheet. This computational research may provide a different point of view to examine all possible parameters that may contribute to the development of AD and T2D and provide a better understanding of the pathological link between these two severe diseases.


Subject(s)
Amyloid beta-Peptides/metabolism , Histidine/metabolism , Islet Amyloid Polypeptide/metabolism , Humans , Molecular Dynamics Simulation , Peptide Fragments/metabolism , Protein Conformation, beta-Strand/physiology
2.
Int J Mol Sci ; 22(21)2021 Oct 20.
Article in English | MEDLINE | ID: mdl-34768745

ABSTRACT

Insoluble protein aggregates with fibrillar morphology called amyloids and ß-barrel proteins both share a ß-sheet-rich structure. Correctly folded ß-barrel proteins can not only function in monomeric (dimeric) form, but also tend to interact with one another-followed, in several cases, by formation of higher order oligomers or even aggregates. In recent years, findings proving that ß-barrel proteins can adopt cross-ß amyloid folds have emerged. Different ß-barrel proteins were shown to form amyloid fibrils in vitro. The formation of functional amyloids in vivo by ß-barrel proteins for which the amyloid state is native was also discovered. In particular, several prokaryotic and eukaryotic proteins with ß-barrel domains were demonstrated to form amyloids in vivo, where they participate in interspecies interactions and nutrient storage, respectively. According to recent observations, despite the variety of primary structures of amyloid-forming proteins, most of them can adopt a conformational state with the ß-barrel topology. This state can be intermediate on the pathway of fibrillogenesis ("on-pathway state"), or can be formed as a result of an alternative assembly of partially unfolded monomers ("off-pathway state"). The ß-barrel oligomers formed by amyloid proteins possess toxicity, and are likely to be involved in the development of amyloidoses, thus representing promising targets for potential therapy of these incurable diseases. Considering rapidly growing discoveries of the amyloid-forming ß-barrels, we may suggest that their real number and diversity of functions are significantly higher than identified to date, and represent only "the tip of the iceberg". Here, we summarize the data on the amyloid-forming ß-barrel proteins, their physicochemical properties, and their biological functions, and discuss probable means and consequences of the amyloidogenesis of these proteins, along with structural relationships between these two widespread types of ß-folds.


Subject(s)
Amyloid/physiology , Protein Aggregates/physiology , Protein Conformation, beta-Strand/physiology , Amyloid/metabolism , Amyloid beta-Peptides/metabolism , Amyloidogenic Proteins/metabolism , Amyloidosis/metabolism , Humans , Molecular Dynamics Simulation , Protein Aggregates/genetics
3.
Molecules ; 26(6)2021 Mar 11.
Article in English | MEDLINE | ID: mdl-33799657

ABSTRACT

Noncovalent interactions play a pivotal role in regulating protein conformation, stability and dynamics. Among the quantum mechanical (QM) overlap-based noncovalent interactions, n→π* is the best understood with studies ranging from small molecules to ß-turns of model proteins such as GB1. However, these investigations do not explore the interplay between multiple overlap interactions in contributing to local structure and stability. In this work, we identify and characterize all noncovalent overlap interactions in the ß-turn, an important secondary structural element that facilitates the folding of a polypeptide chain. Invoking a QM framework of natural bond orbitals, we demonstrate the role of several additional interactions such as n→σ* and π→π* that are energetically comparable to or larger than n→π*. We find that these interactions are sensitive to changes in the side chain of the residues in the ß-turn of GB1, suggesting that the n→π* may not be the only component in dictating ß-turn conformation and stability. Furthermore, a database search of n→σ* and π→π* in the PDB reveals that they are prevalent in most proteins and have significant interaction energies (∼1 kcal/mol). This indicates that all overlap interactions must be taken into account to obtain a comprehensive picture of their contributions to protein structure and energetics. Lastly, based on the extent of QM overlaps and interaction energies, we propose geometric criteria using which these additional interactions can be efficiently tracked in broad database searches.


Subject(s)
Protein Conformation, beta-Strand/physiology , Proteins/chemistry , Hydrogen Bonding , Models, Molecular , Peptides/chemistry , Protein Conformation , Protein Stability , Thermodynamics
4.
Proc Natl Acad Sci U S A ; 118(16)2021 04 20.
Article in English | MEDLINE | ID: mdl-33846247

ABSTRACT

The P-loop Walker A motif underlies hundreds of essential enzyme families that bind nucleotide triphosphates (NTPs) and mediate phosphoryl transfer (P-loop NTPases), including the earliest DNA/RNA helicases, translocases, and recombinases. What were the primordial precursors of these enzymes? Could these large and complex proteins emerge from simple polypeptides? Previously, we showed that P-loops embedded in simple ßα repeat proteins bind NTPs but also, unexpectedly so, ssDNA and RNA. Here, we extend beyond the purely biophysical function of ligand binding to demonstrate rudimentary helicase-like activities. We further constructed simple 40-residue polypeptides comprising just one ß-(P-loop)-α element. Despite their simplicity, these P-loop prototypes confer functions such as strand separation and exchange. Foremost, these polypeptides unwind dsDNA, and upon addition of NTPs, or inorganic polyphosphates, release the bound ssDNA strands to allow reformation of dsDNA. Binding kinetics and low-resolution structural analyses indicate that activity is mediated by oligomeric forms spanning from dimers to high-order assemblies. The latter are reminiscent of extant P-loop recombinases such as RecA. Overall, these P-loop prototypes compose a plausible description of the sequence, structure, and function of the earliest P-loop NTPases. They also indicate that multifunctionality and dynamic assembly were key in endowing short polypeptides with elaborate, evolutionarily relevant functions.


Subject(s)
AAA Domain/genetics , AAA Domain/physiology , Amino Acid Motifs/physiology , Amino Acid Sequence/genetics , DNA Helicases/metabolism , DNA Helicases/physiology , DNA, Single-Stranded/chemistry , DNA, Single-Stranded/metabolism , Models, Molecular , Nucleoside-Triphosphatase/chemistry , Peptides/chemistry , Phosphates/chemistry , Protein Conformation, alpha-Helical/physiology , Protein Conformation, beta-Strand/physiology , Proteins/chemistry , RNA/chemistry , Rec A Recombinases/metabolism
5.
Biochemistry ; 60(6): 431-439, 2021 02 16.
Article in English | MEDLINE | ID: mdl-33533248

ABSTRACT

The field of de novo protein design has met with considerable success over the past few decades. Heme, a cofactor, has often been introduced to impart a diverse array of functions to a protein, ranging from electron transport to respiration. In nature, heme is found to occur predominantly in α-helical structures over ß-sheets, which has resulted in significant designs of heme proteins utilizing coiled-coil helices. By contrast, there are only a few known ß-sheet proteins that bind heme and designs of ß-sheets frequently result in amyloid-like aggregates. This review reflects on our success in designing a series of multistranded ß-sheet heme binding peptides that are well folded in both aqueous and membrane-like environments. Initially, we designed a ß-hairpin peptide that self-assembles to bind heme and performs peroxidase activity in membrane. The ß-hairpin was optimized further to accommodate a heme binding pocket within multistranded ß-sheets for catalysis and electron transfer in membranes. Furthermore, we de novo designed and characterized ß-sheet peptides and miniproteins that are soluble in an aqueous environment capable of binding single and multiple hemes with high affinity and stability. Collectively, these studies highlight the substantial progress made toward the design of functional ß-sheets.


Subject(s)
Hemeproteins/chemistry , Protein Conformation, beta-Strand/physiology , Protein Engineering/methods , Amino Acid Sequence , Circular Dichroism , Heme/chemistry , Heme/metabolism , Hemeproteins/metabolism , Oxidation-Reduction , Peptides/chemistry , Protein Folding , Protein Structure, Secondary/physiology
6.
Methods Mol Biol ; 2251: 205-214, 2021.
Article in English | MEDLINE | ID: mdl-33481242

ABSTRACT

PROPPINs (ß-propellers that bind polyphosphoinositides) are a protein family that binds preferentially phosphatidylinositol 3-phosphate (PtdIns(3)P) and phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2) via its FRRG motif. PROPPINs are involved in autophagic functions, but their molecular mechanism is still elusive. To unravel the molecular mechanism of PROPPINs, it is essential to understand the PROPPIN-phosphoinositide binding. Here, we describe a protocol to study the kinetics of the PROPPIN-phosphoinositide binding using a fluorescence resonance energy transfer (FRET) stopped-flow approach. We use FRET between fluorophore-labeled protein and fluorophore-labeled liposomes, monitoring the increase of the acceptor emission in labeled liposomes after the protein-membrane binding. Through this approach, we studied the kinetics of the PROPPIN Atg18 (Autophagy-related protein 18) from Pichia angusta (PaAtg18) and a mutant of its FRRG motif, called FTTG mutant. Stopped-flow experiments demonstrated that the main function of the FRRG motif is to retain, instead of to drive, Atg18 to the membrane, decreasing the Atg18 dissociation rate. Furthermore, this method is suitable for the study of other PI-binding proteins.


Subject(s)
Autophagy-Related Proteins/pharmacokinetics , Fluorescence Resonance Energy Transfer/methods , Membrane Proteins/pharmacokinetics , Protein Binding/physiology , Saccharomyces cerevisiae Proteins/pharmacokinetics , Autophagy , Autophagy-Related Proteins/metabolism , Carrier Proteins/metabolism , Membrane Proteins/metabolism , Phosphatidylinositol Phosphates/metabolism , Phosphatidylinositols/metabolism , Protein Conformation, beta-Strand/physiology , Protein Domains/physiology , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomycetales/metabolism , Spectrometry, Fluorescence/methods , Vacuoles/metabolism
7.
Molecules ; 25(24)2020 Dec 21.
Article in English | MEDLINE | ID: mdl-33371481

ABSTRACT

The osteogenic differentiation of stem cells is profoundly affected by their microenvironmental conditions. The differentiation behavior of stem cells can be tuned by changing the niche environments. The proteins or peptides that are derived by living organisms facilitate the osteogenic differentiation of stem cells. Here, we have evaluated the osteoinductive and antioxidative potential of the Protaetia brevitarsis seulensis insect-derived protein for human bone marrow-derived mesenchymal stem cells (hBMSCs). The amino acid contents in the isolated protein were determined by an amino acid analyzer. Fourier transform infrared (FTIR) spectroscopy and scanning electron microscopy (SEM) were used to analyze the extract's functional groups and surface morphology. The extracted protein exhibited 51.08% ß-sheet conformation. No adverse effects were observed in extract-treated cells, indicating their biocompatibility. The protein isolate showed an excellent antioxidative property. Besides this, an enhancement in the hBMSCs' mineralization has been observed in the presence of treated protein isolates. Notably, osteogenic marker genes and proteins were effectively expressed in the treated cells. These results indicated that the P. brevitarsis-derived protein isolate can be used as a potential antioxidative biomaterial for bone tissue engineering applications.


Subject(s)
Antioxidants/metabolism , Coleoptera/metabolism , Insect Proteins/metabolism , Amino Acids/metabolism , Animals , Bone and Bones/metabolism , Bone and Bones/physiology , Cell Differentiation/physiology , Cell Line , Humans , Larva/metabolism , Mesenchymal Stem Cells/metabolism , Mesenchymal Stem Cells/physiology , Microscopy, Electron, Scanning/methods , Osteogenesis/physiology , Peptides/metabolism , Protein Conformation, beta-Strand/physiology , Spectroscopy, Fourier Transform Infrared/methods , Tissue Engineering/methods
8.
PLoS One ; 15(12): e0244315, 2020.
Article in English | MEDLINE | ID: mdl-33378364

ABSTRACT

Secondary structure elements are generally found in almost all protein structures revealed so far. In general, there are more ß-sheets than α helices found inside the protein structures. For example, considering the PDB, DSSP and Stride definitions for secondary structure elements and by using the consensus among those, we found 60,727 helices in 4,376 chains identified in all-α structures and 129,440 helices in 7,898 chains identified in all-α and α + ß structures. For ß-sheets, we identified 837,345 strands in 184,925 ß-sheets located within 50,803 chains of all-ß structures and 1,541,961 strands in 355,431 ß-sheets located within 86,939 chains in all-ß and α + ß structures (data extracted on February 1, 2019). In this paper we would first like to address a full characterization of the nanoenvironment found at beta sheet locations and then compare those characteristics with the ones we already published for alpha helical secondary structure elements. For such characterization, we use here, as in our previous work about alpha helical nanoenvironments, set of STING protein structure descriptors. As in the previous work, we assume that we will be able to prove that there is a set of protein structure parameters/attributes/descriptors, which could fully describe the nanoenvironment around beta sheets and that appropriate statistically analysis will point out to significant changes in values for those parameters when compared for loci considered inside and outside defined secondary structure element. Clearly, while the univariate analysis is straightforward and intuitively understood, it is severely limited in coverage: it could be successfully applied at best in up to 25% of studied cases. The indication of the main descriptors for the specific secondary structure element (SSE) by means of the multivariate MANOVA test is the strong statistical tool for complete discrimination among the SSEs, and it revealed itself as the one with the highest coverage. The complete description of the nanoenvironment, by analogy, might be understood in terms of describing a key lock system, where all lock mini cylinders need to combine their elevation (controlled by a matching key) to open the lock. The main idea is as follows: a set of descriptors (cylinders in the key-lock example) must precisely combine their values (elevation) to form and maintain a specific secondary structure element nanoenvironment (a required condition for a key being able to open a lock).


Subject(s)
Protein Conformation, alpha-Helical/physiology , Protein Conformation, beta-Strand/physiology , Protein Structure, Secondary/physiology , Algorithms , Animals , Databases, Protein , Humans , Models, Molecular , Protein Conformation , Proteins/chemistry , Software
9.
Proc Natl Acad Sci U S A ; 117(46): 28775-28783, 2020 11 17.
Article in English | MEDLINE | ID: mdl-33148805

ABSTRACT

Although folded proteins are commonly depicted as simplistic combinations of ß-strands and α-helices, the actual properties and functions of these secondary-structure elements in their native contexts are just partly understood. The principal reason is that the behavior of individual ß- and α-elements is obscured by the global folding cooperativity. In this study, we have circumvented this problem by designing frustrated variants of the mixed α/ß-protein S6, which allow the structural behavior of individual ß-strands and α-helices to be targeted selectively by stopped-flow kinetics, X-ray crystallography, and solution-state NMR. Essentially, our approach is based on provoking intramolecular "domain swap." The results show that the α- and ß-elements have quite different characteristics: The swaps of ß-strands proceed via global unfolding, whereas the α-helices are free to swap locally in the native basin. Moreover, the α-helices tend to hybridize and to promote protein association by gliding over to neighboring molecules. This difference in structural behavior follows directly from hydrogen-bonding restrictions and suggests that the protein secondary structure defines not only tertiary geometry, but also maintains control in function and structural evolution. Finally, our alternative approach to protein folding and native-state dynamics presents a generally applicable strategy for in silico design of protein models that are computationally testable in the microsecond-millisecond regime.


Subject(s)
Protein Conformation, alpha-Helical/physiology , Protein Conformation, beta-Strand/physiology , Protein Structure, Secondary/physiology , Crystallography, X-Ray/methods , Hydrogen Bonding , Kinetics , Protein Conformation , Protein Denaturation , Protein Folding , Proteins/chemistry , Thermodynamics
10.
J Struct Biol ; 212(1): 107593, 2020 10 01.
Article in English | MEDLINE | ID: mdl-32736072

ABSTRACT

Akkermansia muciniphila is a beneficial microorganism colonized in the human gut that can reverse many intestinal metabolic-related diseases. Amuc_1100 is an outer-membrane protein of A. muciniphila. Oral administration of Amuc_1100 can reduce fat mass development, insulin resistance, and dyslipidemia in mice and activated the toll-like receptor 2 (TLR2) to regulate the immune response of the host, but the molecular mechanism remains unclear. Here we report the crystal structure of the extramembranous domain of Amuc_1100, which consists of a four-stranded antiparallel ß-sheet and four α-helices. Two C-terminal helices and the four-stranded antiparallel ß-sheet formed two "αßß" motifs and constituted the core domain, which shared a similar fold with type IV pili and type II Secretion system protein. Although the full-length of the extramembranous domain of Amuc_1100 existed as a monomer in solution, they formed trimer in the crystal. Elimination of the N-terminal coiled-coil helix α1 led to dimerization of Amuc_1100 both in solution and in crystal, indicating that the oligomeric state of Amuc_1100 was variable and could be influenced by α1. In addition, we identified that Amuc_1100 could directly bind human TLR2 (hTRL2) in vitro, suggesting that Amuc_1100 may serve as a new ligand for hTLR2. Dimerization of Amuc_1100 improved its hTLR2-binding affinity, suggesting that the α1-truncated Amuc_1100 could be a beneficial candidate for the development of A. muciniphila related drugs.


Subject(s)
Bacterial Outer Membrane Proteins/chemistry , Bacterial Outer Membrane Proteins/metabolism , Akkermansia/metabolism , Bacterial Secretion Systems/metabolism , Humans , Protein Conformation, alpha-Helical/physiology , Protein Conformation, beta-Strand/physiology , Protein Domains/physiology , Toll-Like Receptor 2/metabolism
11.
Cytoskeleton (Hoboken) ; 77(9): 351-361, 2020 09.
Article in English | MEDLINE | ID: mdl-32845074

ABSTRACT

In in vitro microtubule gliding assays, most kinesins drive the rotation of gliding microtubules around their longitudinal axes in a corkscrew motion. The corkscrewing pitch is smaller than the supertwisted protofilament pitch of microtubules, indicating that the corkscrewing pitch is an inherent property of kinesins. To elucidate the molecular mechanisms through which kinesins corkscrew the microtubule, we performed three-dimensional tracking of a quantum dot bound to a microtubule translocating over a surface coated with single-headed kinesin-1 s under various assay conditions to alter the interactions between the kinesin and microtubule. Although alternations in kinesin concentration, ionic strength, and ATP concentration changed both gliding and rotational velocities, the corkscrewing pitch remained left-handed and constant at ~0.3 µm under all tested conditions apart from a slight increase in pitch at a low ATP concentration. We then used our system to analyze the effect of point mutations in the N-terminal ß-strand protruding from the kinesin motor core and found mutations that decreased the corkscrewing pitch. Our findings confirmed that the corkscrewing motion of microtubules is caused by the intrinsic properties of the kinesin and demonstrates that changes in the active or retarding force originating from the N-terminal ß-strand in the head modulate the pitch.


Subject(s)
Kinesins/metabolism , Protein Conformation, beta-Strand/physiology , Humans
12.
J Struct Biol ; 212(1): 107605, 2020 10 01.
Article in English | MEDLINE | ID: mdl-32805410

ABSTRACT

BCP1 is a protein enriched in the nucleus that is required for Mss4 nuclear export and identified as the chaperone of ribosomal protein Rpl23 in Saccharomyces cerevisiae. According to sequence homology, BCP1 is related to the mammalian BRCA2-interacting protein BCCIP and belongs to the BCIP protein family (PF13862) in the Pfam database. However, the BCIP family has no discernible similarity to proteins with known structure. Here, we report the crystal structure of BCP1, presenting an α/ß fold in which the central antiparallel ß-sheet is flanked by helices. Protein structural classification revealed that BCP1 has similarity to the GNAT superfamily but no conserved substrate-binding residues. Further modeling and protein-protein docking work provide a plausible model to explain the interaction between BCP1 and Rpl23. Our structural analysis presents the first structure of BCIP family and provides a foundation for understanding the molecular basis of BCP1 as a chaperone of Rpl23 for ribosome biosynthesis.


Subject(s)
Nuclear Proteins/chemistry , Nuclear Proteins/metabolism , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/metabolism , Binding Sites/physiology , Crystallography, X-Ray/methods , Protein Conformation, beta-Strand/physiology , Protein Structure, Secondary/physiology , Ribosomal Proteins/chemistry , Ribosomal Proteins/metabolism , Ribosomes/metabolism
13.
Immunity ; 53(1): 106-114.e5, 2020 07 14.
Article in English | MEDLINE | ID: mdl-32553275

ABSTRACT

The recognition and cleavage of gasdermin D (GSDMD) by inflammatory caspases-1, 4, 5, and 11 are essential steps in initiating pyroptosis after inflammasome activation. Previous work has identified cleavage site signatures in substrates such as GSDMD, but it is unclear whether these are the sole determinants for caspase engagement. Here we report the crystal structure of a complex between human caspase-1 and the full-length murine GSDMD. In addition to engagement of the GSDMD N- and C-domain linker by the caspase-1 active site, an anti-parallel ß sheet at the caspase-1 L2 and L2' loops bound a hydrophobic pocket within the GSDMD C-terminal domain distal to its N-terminal domain. This "exosite" interface endows an additional function for the GSDMD C-terminal domain as a caspase-recruitment module besides its role in autoinhibition. Our study thus reveals dual-interface engagement of GSDMD by caspase-1, which may be applicable to other physiological substrates of caspases.


Subject(s)
Caspase 1/metabolism , Catalytic Domain/physiology , Intracellular Signaling Peptides and Proteins/metabolism , Phosphate-Binding Proteins/metabolism , Pyroptosis/immunology , Animals , Cell Line , Crystallography, X-Ray , HEK293 Cells , Humans , Hydrophobic and Hydrophilic Interactions , Inflammasomes/immunology , Mice , Protein Binding/physiology , Protein Conformation, beta-Strand/physiology , THP-1 Cells
14.
Biochemistry ; 59(10): 1093-1103, 2020 03 17.
Article in English | MEDLINE | ID: mdl-32100530

ABSTRACT

Epigallocatechin-3-gallate (EGCG) is a catechin found in green tea that can inhibit the amyloid formation of a wide variety of proteins. EGCG's ability to prevent or redirect the amyloid formation of so many proteins may reflect a common mechanism of action, and thus, greater molecular-level insight into how it exerts its effect could have broad implications. Here, we investigate the molecular details of EGCG's inhibition of the protein ß-2-microglobulin (ß2m), which forms amyloids in patients undergoing long-term dialysis treatment. Using size-exclusion chromatography and a collection of mass spectrometry-based techniques, we find that EGCG prevents Cu(II)-induced ß2m amyloid formation by diverting the normal progression of preamyloid oligomers toward the formation of spherical, redissolvable aggregates. EGCG exerts its effect by binding with a micromolar affinity (Kd ≈ 5 µM) to the ß2m monomer on the edge of two ß-sheets near the N-terminus. This interaction destabilizes the preamyloid dimer and prevents the formation of a tetramer species previously shown to be essential for Cu(II)-induced ß2m amyloid formation. EGCG's binding at the edge of the ß-sheets in ß2m is consistent with a previous hypothesis that EGCG generally prevents amyloid formation by binding cross-ß-sheet aggregation intermediates.


Subject(s)
Amyloid/chemistry , Catechin/analogs & derivatives , beta 2-Microglobulin/chemistry , Amyloid/metabolism , Amyloidogenic Proteins/chemistry , Amyloidosis/metabolism , Catechin/metabolism , Catechin/pharmacology , Catechin/physiology , Chromatography, Gel/methods , Copper/metabolism , Humans , Mass Spectrometry/methods , Models, Molecular , Protein Conformation, beta-Strand/physiology , Protein Multimerization/drug effects , beta 2-Microglobulin/antagonists & inhibitors , beta 2-Microglobulin/metabolism
15.
Biochemistry ; 58(30): 3302-3313, 2019 07 30.
Article in English | MEDLINE | ID: mdl-31283187

ABSTRACT

Thymidylate synthase (TS) is a dimeric enzyme conserved in all life forms that exhibits the allosteric feature of half-the-sites activity. Neither the reason for nor the mechanism of this phenomenon is understood. We used a combined nuclear magnetic resonance (NMR) and molecular dynamics approach to study a stable intermediate preceding hydride transfer, which is the rate-limiting and half-the-sites step. In NMR titrations with ligands leading to this intermediate, we measured chemical shifts of the apoenzyme (lig0), the saturated holoenzyme (lig2), and the typically elusive singly bound (lig1) states. Approximately 40 amides showed quartet patterns providing direct NMR evidence of coupling between the active site and probes >30 Å away in the distal subunit. Quartet peak patterns have symmetrical character, indicating reciprocity in communicating the first and second binding events to the distal protomer. Quartets include key catalytic residues and map to the dimer interface ß-sheet, which also represents the shortest path between the two active sites. Simulations corroborate the coupling observed in solution in that there is excellent overlap between quartet residues and main-chain atoms having intersubunit cross-correlated motions. Simulations identify five hot spot residues, three of which lie at the kink in the unique ß-bulge abutting the active sites on either end of the sheet. Interstrand cross-correlated motions become more organized and pronounced as the enzyme progresses from lig0 to lig1 and ultimately lig2. Coupling in the apparently symmetrical complex has implications for half-the-sites reactivity and potentially resolves the paradox of inequivalent TS active sites despite the vast majority of X-ray structures appearing to be symmetrical.


Subject(s)
Protein Multimerization/physiology , Thymidylate Synthase/chemistry , Thymidylate Synthase/metabolism , Catalytic Domain/physiology , Protein Conformation, beta-Strand/physiology , Protein Structure, Secondary , Protein Structure, Tertiary
16.
Article in English | MEDLINE | ID: mdl-30617049

ABSTRACT

Polyphosphate (polyP), an extremely simple polyanion, has long been known to be involved in a variety of different cellular processes, ranging from stress resistance, biofilm formation, and virulence in bacteria to bone mineralization, blood clotting, and mammalian target of rapamycin (mTOR) signaling in mammalian organisms. Our laboratory recently discovered a completely unexpected role of polyP as a stabilizing scaffold for ß-sheet-containing protein-folding intermediates. This realization led us to investigate the effects of polyP on amyloidogenic processes and the novel concept that polyP might play a role in neurodegenerative diseases. In this review, we will summarize recent results that show that polyP is a physiological modifier that accelerates amyloid fiber formation, alters fiber morphology, and protects cells against amyloid toxicity. We will review the current knowledge on the distribution, levels, and roles of polyP in the mammalian brain, and discuss potential mechanisms by which polyP might ameliorate amyloid toxicity.


Subject(s)
Amyloid/metabolism , Polyphosphates/metabolism , Protein Conformation, beta-Strand/physiology , Animals , Brain/metabolism , Cell Survival , Humans
17.
J Mol Biol ; 431(2): 289-307, 2019 01 18.
Article in English | MEDLINE | ID: mdl-30419243

ABSTRACT

Type VII secretion systems (ESX) are responsible for transport of multiple proteins in mycobacteria. How different ESX systems achieve specific secretion of cognate substrates remains elusive. In the ESX systems, the cytoplasmic chaperone EspG forms complexes with heterodimeric PE-PPE substrates that are secreted from the cells or remain associated with the cell surface. Here we report the crystal structure of the EspG1 chaperone from the ESX-1 system determined using a fusion strategy with T4 lysozyme. EspG1 adopts a quasi 2-fold symmetric structure that consists of a central ß-sheet and two α-helical bundles. In addition, we describe the structures of EspG3 chaperones from four different crystal forms. Alternate conformations of the putative PE-PPE binding site are revealed by comparison of the available EspG3 structures. Analysis of EspG1, EspG3, and EspG5 chaperones using small-angle X-ray scattering reveals that EspG1 and EspG3 chaperones form dimers in solution, which we observed in several of our crystal forms. Finally, we propose a model of the ESX-3 specific EspG3-PE5-PPE4 complex based on the small-angle X-ray scattering analysis.


Subject(s)
Antigens, Bacterial/metabolism , Bacterial Proteins/metabolism , Molecular Chaperones/metabolism , Mycobacterium tuberculosis/metabolism , Type VII Secretion Systems/metabolism , Virulence Factors/metabolism , Amino Acid Sequence , Binding Sites/physiology , Protein Conformation , Protein Conformation, alpha-Helical/physiology , Protein Conformation, beta-Strand/physiology
18.
Neurobiol Aging ; 72: 98-105, 2018 12.
Article in English | MEDLINE | ID: mdl-30240946

ABSTRACT

The assembly of Tau into abundant ß-sheet-rich filaments characterizes human tauopathies. A pathological pathway leading from monomeric to filamentous Tau is believed to be at the heart of these diseases. However, in Drosophila models of Tauopathy, neurodegeneration has been observed in the absence of abundant Tau filaments. Here we investigated the role of Tau assembly into ß-sheets by expressing wild-type and Δ306-311 human Tau-383 in the retina and brain of Drosophila. We analyzed both lines for eye abnormalities, brain vacuolization, Tau phosphorylation and assembly, as well as climbing activity and survival. Flies expressing wild-type Tau-383 showed MC-1 staining, Tau hyperphosphorylation, and neurodegeneration. By contrast, flies expressing Δ306-311 Tau-383 had less MC-1 staining, reduced Tau hyperphosphorylation, and no detectable neurodegeneration. Their climbing ability and lifespan were similar to those of nontransgenic flies. Fluorescence spectroscopy after addition of Thioflavin T, a dye that interacts with ß-sheets, showed no signal when Δ306-311 Tau-383 was incubated with heparin. These findings demonstrate that the assembly of Tau into ß-sheets is necessary for neurodegeneration.


Subject(s)
Brain/metabolism , Drosophila melanogaster/metabolism , Neurodegenerative Diseases/metabolism , Retina/metabolism , tau Proteins/metabolism , Animals , Animals, Genetically Modified , Behavior, Animal/physiology , Brain/pathology , Disease Models, Animal , Humans , Neurodegenerative Diseases/pathology , Phosphorylation , Protein Conformation, beta-Strand/physiology , Retina/pathology
19.
Nat Commun ; 9(1): 2121, 2018 05 29.
Article in English | MEDLINE | ID: mdl-29844575

ABSTRACT

The ß-sheet is the key structure underlying the excellent mechanical properties of spider silk. However, the comprehensive mechanism underlying ß-sheet formation from soluble silk proteins during the transition into insoluble stable fibers has not been elucidated. Notably, the assembly of repetitive domains that dominate the length of the protein chains and structural features within the spun fibers has not been clarified. Here we determine the conformation and dynamics of the soluble precursor of the repetitive domain of spider silk using solution-state NMR, far-UV circular dichroism and vibrational circular dichroism. The soluble repetitive domain contains two major populations: ~65% random coil and ~24% polyproline type II helix (PPII helix). The PPII helix conformation in the glycine-rich region is proposed as a soluble prefibrillar region that subsequently undergoes intramolecular interactions. These findings unravel the mechanism underlying the initial step of ß-sheet formation, which is an extremely rapid process during spider silk assembly.


Subject(s)
Protein Conformation, beta-Strand/physiology , Silk/chemistry , Spiders/metabolism , Animals , Circular Dichroism , Magnetic Resonance Spectroscopy , Stress, Mechanical , Tensile Strength/physiology
20.
EMBO J ; 37(3): 337-350, 2018 02 01.
Article in English | MEDLINE | ID: mdl-29247078

ABSTRACT

Protein aggregation is associated with neurodegeneration and various other pathologies. How specific cellular environments modulate the aggregation of disease proteins is not well understood. Here, we investigated how the endoplasmic reticulum (ER) quality control system handles ß-sheet proteins that were designed de novo to form amyloid-like fibrils. While these proteins undergo toxic aggregation in the cytosol, we find that targeting them to the ER (ER-ß) strongly reduces their toxicity. ER-ß is retained within the ER in a soluble, polymeric state, despite reaching very high concentrations exceeding those of ER-resident molecular chaperones. ER-ß is not removed by ER-associated degradation (ERAD) but interferes with ERAD of other proteins. These findings demonstrate a remarkable capacity of the ER to prevent the formation of insoluble ß-aggregates and the secretion of potentially toxic protein species. Our results also suggest a generic mechanism by which proteins with exposed ß-sheet structure in the ER interfere with proteostasis.


Subject(s)
Amyloidogenic Proteins/metabolism , Endoplasmic Reticulum-Associated Degradation/physiology , Endoplasmic Reticulum/metabolism , Protein Aggregation, Pathological/prevention & control , Cell Line, Tumor , HEK293 Cells , HeLa Cells , Humans , Molecular Chaperones/metabolism , Protein Aggregation, Pathological/pathology , Protein Conformation, beta-Strand/physiology , Protein Folding , RNA Interference , RNA, Small Interfering/genetics , Unfolded Protein Response/physiology
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