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Methods in Enzymology 2016Allosteric networks allow enzymes to transmit information and regulate their catalytic activities over vast distances. In principle, molecular dynamics (MD) simulations... (Review)
Review
Allosteric networks allow enzymes to transmit information and regulate their catalytic activities over vast distances. In principle, molecular dynamics (MD) simulations can be used to reveal the mechanisms that underlie this phenomenon; in practice, it can be difficult to discern allosteric signals from MD trajectories. Here, we describe how MD simulations can be analyzed to reveal correlated motions and allosteric networks, and provide an example of their use on the coagulation enzyme thrombin. Methods are discussed for calculating residue-pair correlations from atomic fluctuations and mutual information, which can be combined with contact information to identify allosteric networks and to dynamically cluster a system into highly correlated communities. In the case of thrombin, these methods show that binding of the antagonist hirugen significantly alters the enzyme's correlation landscape through a series of pathways between Exosite I and the catalytic core. Results suggest that hirugen binding curtails dynamic diversity and enforces stricter venues of influence, thus reducing the accessibility of thrombin to other molecules.
Topics: Allosteric Regulation; Allosteric Site; Catalytic Domain; Chlorides; Heparin; Hirudins; Humans; Molecular Dynamics Simulation; Peptide Fragments; Protein Binding; Protein Conformation, alpha-Helical; Protein Conformation, beta-Strand; Protein Interaction Domains and Motifs; Sodium; Thrombin; Water
PubMed: 27497176
DOI: 10.1016/bs.mie.2016.05.027 -
Biomacromolecules May 2021Peptides and their conjugates (to lipids, bulky N-terminals, or other groups) can self-assemble into nanostructures such as fibrils, nanotubes, coiled coil bundles, and... (Review)
Review
Peptides and their conjugates (to lipids, bulky N-terminals, or other groups) can self-assemble into nanostructures such as fibrils, nanotubes, coiled coil bundles, and micelles, and these can be used as platforms to present functional residues in order to catalyze a diversity of reactions. Peptide structures can be used to template catalytic sites inspired by those present in natural enzymes as well as simpler constructs using individual catalytic amino acids, especially proline and histidine. The literature on the use of peptide (and peptide conjugate) α-helical and β-sheet structures as well as turn or disordered peptides in the biocatalysis of a range of organic reactions including hydrolysis and a variety of coupling reactions (e.g., aldol reactions) is reviewed. The simpler design rules for peptide structures compared to those of folded proteins permit ready design (minimalist approach) of effective catalytic structures that mimic the binding pockets of natural enzymes or which simply present catalytic motifs at high density on nanostructure scaffolds. Research on these topics is summarized, along with a discussion of metal nanoparticle catalysts templated by peptide nanostructures, especially fibrils. Research showing the high activities of different classes of peptides in catalyzing many reactions is highlighted. Advances in peptide design and synthesis methods mean they hold great potential for future developments of effective bioinspired and biocompatible catalysts.
Topics: Catalysis; Nanostructures; Peptides; Protein Conformation, alpha-Helical; Protein Conformation, beta-Strand
PubMed: 33843196
DOI: 10.1021/acs.biomac.1c00240 -
Current Opinion in Genetics &... Apr 2021Eukaryotic cells express thousands of protein domains long believed to function in the absence of molecular order. These intrinsically disordered protein (IDP) domains... (Review)
Review
Eukaryotic cells express thousands of protein domains long believed to function in the absence of molecular order. These intrinsically disordered protein (IDP) domains are typified by gibberish-like repeats of only a limited number of amino acids that we refer to as domains of low sequence complexity. A decade ago, it was observed that these low complexity (LC) domains can undergo phase transition out of aqueous solution to form either liquid-like droplets or hydrogels. The self-associative interactions responsible for phase transition involve the formation of specific cross-β structures that are unusual in being labile to dissociation. Here we give evidence that the LC domains of two RNA binding proteins, ataxin-2 and TDP43, form cross-β interactions that specify biologically relevant redox sensors.
Topics: Amino Acid Sequence; Ataxin-2; DNA-Binding Proteins; Eukaryotic Cells; Gene Expression Regulation; Intrinsically Disordered Proteins; Oxidation-Reduction; Protein Conformation, beta-Strand; Protein Domains; RNA-Binding Proteins
PubMed: 33454579
DOI: 10.1016/j.gde.2020.12.006 -
Nature Structural & Molecular Biology Nov 2018β-sheet proteins carry out critical functions in biology, and hence are attractive scaffolds for computational protein design. Despite this potential, de novo design of...
β-sheet proteins carry out critical functions in biology, and hence are attractive scaffolds for computational protein design. Despite this potential, de novo design of all-β-sheet proteins from first principles lags far behind the design of all-α or mixed-αβ domains owing to their non-local nature and the tendency of exposed β-strand edges to aggregate. Through study of loops connecting unpaired β-strands (β-arches), we have identified a series of structural relationships between loop geometry, side chain directionality and β-strand length that arise from hydrogen bonding and packing constraints on regular β-sheet structures. We use these rules to de novo design jellyroll structures with double-stranded β-helices formed by eight antiparallel β-strands. The nuclear magnetic resonance structure of a hyperthermostable design closely matched the computational model, demonstrating accurate control over the β-sheet structure and loop geometry. Our results open the door to the design of a broad range of non-local β-sheet protein structures.
Topics: Amino Acid Sequence; Computer Simulation; Hydrogen Bonding; Models, Molecular; Nuclear Magnetic Resonance, Biomolecular; Protein Conformation; Protein Conformation, beta-Strand; Protein Engineering; Protein Folding; Protein Stability; Proteins
PubMed: 30374087
DOI: 10.1038/s41594-018-0141-6 -
Journal of Molecular Biology Jul 2020We present solid-state NMR measurements of β-strand secondary structure and inter-strand organization within a 150-kDa oligomeric aggregate of the 42-residue variant of...
We present solid-state NMR measurements of β-strand secondary structure and inter-strand organization within a 150-kDa oligomeric aggregate of the 42-residue variant of the Alzheimer's amyloid-β peptide (Aβ(1-42)). We build upon our previous report of a β-strand spanned by residues 30-42, which arranges into an antiparallel β-sheet. New results presented here indicate that there is a second β-strand formed by residues 11-24. Contrary to expectations, NMR data indicate that this second β-strand is organized into a parallel β-sheet despite the co-existence of an antiparallel β-sheet in the same structure. In addition, the in-register parallel β-sheet commonly observed for amyloid fibril structure does not apply to residues 11-24 in the 150-kDa oligomer. Rather, we present evidence for an inter-strand registry shift of three residues that likely alternate in direction between adjacent molecules along the β-sheet. We corroborated this unexpected scheme for β-strand organization using multiple two-dimensional NMR and C-C dipolar recoupling experiments. Our findings indicate a previously unknown assembly pathway and inspire a suggestion as to why this aggregate does not grow to larger sizes.
Topics: Amino Acid Sequence; Amyloid beta-Peptides; Carbon-13 Magnetic Resonance Spectroscopy; Humans; Models, Molecular; Peptide Fragments; Protein Conformation, beta-Strand; Protein Multimerization
PubMed: 32470558
DOI: 10.1016/j.jmb.2020.05.018 -
PloS One 2020Secondary structure elements are generally found in almost all protein structures revealed so far. In general, there are more β-sheets than α helices found inside the...
Secondary structure elements are generally found in almost all protein structures revealed so far. In general, there are more β-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 + β structures. For β-sheets, we identified 837,345 strands in 184,925 β-sheets located within 50,803 chains of all-β structures and 1,541,961 strands in 355,431 β-sheets located within 86,939 chains in all-β and α + β 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).
Topics: Algorithms; Animals; Databases, Protein; Humans; Models, Molecular; Protein Conformation; Protein Conformation, alpha-Helical; Protein Conformation, beta-Strand; Protein Structure, Secondary; Proteins; Software
PubMed: 33378364
DOI: 10.1371/journal.pone.0244315 -
ACS Chemical Neuroscience Aug 2020High-resolution structures of oligomers formed by the β-amyloid peptide, Aβ, are important for understanding the molecular basis of Alzheimer's disease. Dimers of Aβ...
High-resolution structures of oligomers formed by the β-amyloid peptide, Aβ, are important for understanding the molecular basis of Alzheimer's disease. Dimers of Aβ are linked to the pathogenesis and progression of Alzheimer's disease, and tetramers of Aβ are neurotoxic. This paper reports the X-ray crystallographic structures of dimers and tetramers, as well as an octamer, formed by a peptide derived from the central and -terminal regions of Aβ. In the crystal lattice, the peptide assembles to form two different dimers-an antiparallel β-sheet dimer and a parallel β-sheet dimer-that each further self-assemble to form two different tetramers-a sandwich-like tetramer and a twisted β-sheet tetramer. The structures of these dimers and tetramers derived from Aβ serve as potential models for dimers and tetramers of full-length Aβ that form and in Alzheimer's disease-afflicted brains.
Topics: Alzheimer Disease; Amyloid beta-Peptides; Crystallography, X-Ray; Humans; Models, Molecular; Peptide Fragments; Protein Conformation, beta-Strand
PubMed: 32584538
DOI: 10.1021/acschemneuro.0c00290 -
Biomolecules Mar 2022One of the most desirable properties that biomaterials designed for tissue engineering or drug delivery applications should fulfill is biodegradation and resorption...
One of the most desirable properties that biomaterials designed for tissue engineering or drug delivery applications should fulfill is biodegradation and resorption without toxicity. Therefore, there is an increasing interest in the development of biomaterials able to be enzymatically degraded once implanted at the injury site or once delivered to the target organ. In this paper, we demonstrate the protease sensitivity of self-assembling amphiphilic peptides, in particular, RAD16-I (AcN-RADARADARADARADA-CONH), which contains four potential cleavage sites for trypsin. We detected that when subjected to thermal denaturation, the peptide secondary structure suffers a transition from β-sheet to random coil. We also used Matrix-Assisted Laser Desorption/Ionization-Time-Of-Flight (MALDI-TOF) to detect the proteolytic breakdown products of samples subjected to incubation with trypsin as well as atomic force microscopy (AFM) to visualize the effect of the degradation on the nanofiber scaffold. Interestingly, thermally treated samples had a higher extent of degradation than non-denatured samples, suggesting that the transition from β-sheet to random coil leaves the cleavage sites accessible and susceptible to protease degradation. These results indicate that the self-assembling peptide can be reduced to short peptide sequences and, subsequently, degraded to single amino acids, constituting a group of naturally biodegradable materials optimal for their application in tissue engineering and regenerative medicine.
Topics: Biocompatible Materials; Peptide Hydrolases; Peptides; Protein Conformation, beta-Strand; Trypsin
PubMed: 35327603
DOI: 10.3390/biom12030411 -
Journal of the American Chemical Society Oct 2016In this paper, we investigate the coassembly of peptides derived from the central and C-terminal regions of the β-amyloid peptide (Aβ). In the preceding paper, J. Am....
In this paper, we investigate the coassembly of peptides derived from the central and C-terminal regions of the β-amyloid peptide (Aβ). In the preceding paper, J. Am. Chem. Soc. 2016, DOI: 10.1021/jacs.6b06000 , we established that peptides containing residues 17-23 (LVFFAED) from the central region of Aβ and residues 30-36 (AIIGLMV) from the C-terminal region of Aβ assemble to form homotetramers consisting of two hydrogen-bonded dimers. Here, we mix these tetramer-forming peptides and determine how they coassemble. Incorporation of a single N isotopic label into each peptide provides a spectroscopic probe with which to elucidate the coassembly of the peptides by H,N HSQC. Job's method of continuous variation and nonlinear least-squares fitting reveal that the peptides form a mixture of heterotetramers in 3:1, 2:2, and 1:3 stoichiometries, in addition to the homotetramers. These studies also establish the relative stability of each tetramer and show that the 2:2 heterotetramer predominates. N-Edited NOESY shows the 2:2 heterotetramer comprises two different homodimers, rather than two heterodimers. The peptides within the heterotetramer segregate in forming the homodimer subunits, but the two homodimers coassemble in forming the heterotetramer. These studies show that the central and C-terminal regions of Aβ can preferentially segregate within β-sheets and that the resulting segregated β-sheets can further coassemble.
Topics: Amino Acid Sequence; Amyloid beta-Peptides; Isomerism; Molecular Dynamics Simulation; Peptide Fragments; Protein Conformation, beta-Strand; Protein Multimerization
PubMed: 27642763
DOI: 10.1021/jacs.6b06001 -
International Journal of Molecular... Jan 2021The amyloid-β (Aβ) peptides are associated with two prominent diseases in the brain, Alzheimer's disease (AD) and cerebral amyloid angiopathy (CAA). Aβ42 is the...
The amyloid-β (Aβ) peptides are associated with two prominent diseases in the brain, Alzheimer's disease (AD) and cerebral amyloid angiopathy (CAA). Aβ42 is the dominant component of cored parenchymal plaques associated with AD, while Aβ40 is the predominant component of vascular amyloid associated with CAA. There are familial CAA mutations at positions Glu22 and Asp23 that lead to aggressive Aβ aggregation, drive vascular amyloid deposition and result in degradation of vascular membranes. In this study, we compared the transition of the monomeric Aβ40-WT peptide into soluble oligomers and fibrils with the corresponding transitions of the Aβ40-Dutch (E22Q), Aβ40-Iowa (D23N) and Aβ40-Dutch, Iowa (E22Q, D23N) mutants. FTIR measurements show that in a fashion similar to Aβ40-WT, the familial CAA mutants form transient intermediates with anti-parallel β-structure. This structure appears before the formation of cross-β-sheet fibrils as determined by thioflavin T fluorescence and circular dichroism spectroscopy and occurs when AFM images reveal the presence of soluble oligomers and protofibrils. Although the anti-parallel β-hairpin is a common intermediate on the pathway to Aβ fibrils for the four peptides studied, the rate of conversion to cross-β-sheet fibril structure differs for each.
Topics: Alzheimer Disease; Amyloid; Amyloid beta-Peptides; Benzothiazoles; Cerebral Amyloid Angiopathy; Circular Dichroism; Fluorescence; Microscopy, Atomic Force; Mutation; Plaque, Amyloid; Protein Conformation, beta-Strand; Spectroscopy, Fourier Transform Infrared
PubMed: 33513738
DOI: 10.3390/ijms22031225