What is the significance of protein folding




















Protein Eng. Sridhar S, Guruprasad K. Molecular evolution of the homeodomain family of transcription factors. Nucl Acid Res. Experimental and theoretical studies of the effect of the medium on the rotational barriers for N,N-dimethylformamide and N,N-dimethylacetamide.

Protein dielectric constants determined from NMR chemical shift perturbation. Direct measurement of the dielectric polarization properties of DNA. Structural adaptation of extreme halophilic proteins through decrease of conserved hydrophobic contact surface. BMC Struct Biol. Covalency of hydrogen bonds in liquid water can be probed by proton nuclear magnetic resonance experiments.

Modern Electrochemistry Vol 1: Ionics. New York: Plenum Press; Ghosh JC. The abnormality of strong electrolytes. Part 1. Electrical conductivity of aqueous salt solutions. J Chem Soc Trans. Kendall J. The abnormality of strong electrolytes and the ionization theory of Ghosh.

A distinct 14 residue site triggers coiled-coil formation in cortexillin I. EMBO J. Spitzer J, Poolman B. Microbiol Mol Biol Rev. Fast and one-step folding of closely and distantly related homologous proteins of a four-helix bundle family. Microsecond protein folding through a compact transition state. Rapid folding with and without populated intermediates in the homologous four-helix proteins Im7 and Im9. Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation.

Preorganized secondary structure as an important determinant of fast protein folding. Experimental test of villin subdomain folding simulations. Unifying features in protein folding mechanism.

Chem Phys. Microsecond folding dynamics of the F13WG29A mutant of the B domain of staphylococcal protein A by laser-induced temperature jump.

The structure of the major transition state for folding of an FF domain from experiment and simulation. Dodson CA, Arbely E. Protein folding of the SAP domain, a naturally occurring two-helix bundle. FEBS Lett. A helix propensity scale based on experimental studies of peptides and proteins. Padmanabhan S, Baldwin RL. Straight-chain non-polar amino acids are good helix formers in water. Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions.

Helix propensities of basic amino acids increase with the length of the side-chain. Helix propensity of highly fluorinated amino acids.

Helix formation and capping energetics of arginine analogs with varying side chain lengths. Amino Acids. Biophys Chem. Effect of highly fluorinated amino acids on protein stability at a solvent-exposed position on an internal strand of protein G B1 domain.

Thermostable xylanase from Thermoascus auranticus at ultrahigh resolution 0. Probing the role of backbone hydrogen bonds in protein-peptide interactions by amide-to-ester mutations. PDZ domain binding is optimized across the mouse proteome. Quantification of PDZ domain specificity, prediction of ligand affinity and rational design of super-binding peptides. Forces stabilizing proteins.

Contributions of the large hydrophobic amino acids to the stability of staphylococcal nuclease. Contributions of hydrophobic interactions to protein stability. Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect. The response of T4 lysozyme to large-to-small substitutions within its core and its relation to the hydrophobic effect.

The effect of boundary selection on the stability and folding of the third fibronectin type III domain from human tenascin. Two proteins with the same structure respond very differently to mutation: the role of plasticity in protein stability.

Context-dependent nature of destabilizing mutations on the stability of FKPB A measure of helical propensity for amino acids in membrane environments. Nat Struc Biol. Helices and sheets in vacuo. Phys Chem Chem Phys. Understanding nucleic acid-ion interactions.

Annu Rev Biochem. Hydrogen-bonded cooperativity in protein secondary structure. Understanding the dielectric properties of liquid amides from a polarizable force field.

Tuning inflammation and immunity by chemokine sequestration: decoys and more. Nat Rev Immun. Krishna N, Guruprasad K. Certain heptapeptide and large sequences representing an entire helix, strand or coil conformation in proteins are associated as chameleon sequences. Int J Biol Macromol. Evolutionary bridges to new protein folds: design of C-terminal protein chameleon sequences.

Interconversion between two unrelated protein folds in the lymphotactin native state. Mutational tipping points for switching protein folds and functions. A minimal sequence code for switching protein structure and function. The Mad2 spindle checkpoint protein has two distinct natively folded states.

Nat Struc Mol Biol. Exploring the binding diversity of intrinsically disordered proteins involved in one-to-many binding. J Biol Chem. Structural basis for the attachment of a paramyxoviral polymerase to its template.

Multiscaled exploration of coupled folding and binding of an intrinsically disordered molecular recognition element in measles virus nucleoprotein. Structural and dynamical features of inteins and implications on protein splicing. Defining the molecular basis of amyloid inhibitors: human islet amyloid polypeptide-insulin interactions. Structure of influenza hemagglutinin at the pH of membrane fusion. Diphteria toxin conformational switching at acidic pH.

FEBS J. Acidic pH-induced conformational changes in amyloidogenic mutant transthyretin. Structural insight into pH-induced conformational change within the native transthyretin tetramer. Experimentally derived structural constraints for amyloid fibrils of wild-type transthyretin. Structural changes associated with transthyretin misfolding and amyloid formation revealed by solution and solid-state NMR.

Identification of a subunit interface in transthyretin amyloid fibrils: evidence for self-assembly from oligomeric building blocks. Exposure of cryptic epitopes on transthyretin only in amyloid and in amyloidogenic mutants. Probing solvent accessibility of transthyretin amyloid by solution NMR spectroscopy.

Considerably unfolded monomers preceed and exchange with dynamically structured amyloid protofibrils. Sci Rep. A look into amyloid formation by transthyretin: aggregation pathway and a novel kinetic model.

Force spectroscopy reveals the presence of structurally modified dimers in transthyretin amyloid annular oligomers. J Mol Recognit. Eur J Biochem. Is the membrane-spanning domain where we think it is? Chem Commun. J Struct Biol. Vitalis A, Caflisch A. Monomeric amyloid beta peptide in hexafluoroisopropanol detected by small angle neutron scattering.

A partially folded structure of amyloid-beta 1—40 in an aqueous environment. Biochem Biophys Res Comm. Chem Phys Phys Chem. J Neurosci. Garai K, Frieden C. AIP Advances. J Clin Neurosci. ACS Chem. Bio Pharm Bull. Kim W, Hecht MH. Biophysical characterization of longer forms of amyloid beta peptides: possible contribution to flocculent plaque formation.

J Neurochem. Nat Neurosci. Am J Pathol. Acta Neuropathol. Fezoui Y, Teplow DB. J Biol Phys. Sci Adv. Hamley IW. Biochem J. Matsuzaki K. Glabe CG. Structural classification of toxic amyloid oligomers. Neurobiol Dis. Cell Reports. Nat Chem. Nat Struct Mol Biol. Neurodegenerative disease: amyloid pores from pathogenic mutations. Alzheimer peptides aggregate into transient nanoglobules that nucleate fibrils.

Proc Natl Acad Sci. Novel mechanistic insight into the molecular basis of amyloid polymorphism and secondary nucleation during amyloid formation. Tycko R. Amyloid polymorphism: structural basis and neurobiological relevance. Cell Mol Life Sci. A specific amyloid-beta protein assembly in the brain impairs memory.

ACS Chem Neurosci. Ion strength and pH sensitive phase transition of N-isobutyryl-L- D -cysteine monolayers on Au surfaces. Ramachandran G, Udgaonkar JB. Wang Y, Mandelkow E. Tau in physiology and pathology.

Nat Rev Neurosci. Folding of the repeat domain of tau upon binding to lipid surfaces. Tau binds to lipid membrane surfaces via short amphipathic helices located in its microtubule-binding repeats. Folding of the tau protein on microtubules. Tau binds to multiple tubulin dimers with helical structures. Alternative conformations of the tau repeat domain in complex with an engineered binding protein.

A nucleated assembly mechanism of Alzheimer paired helical filaments. Nucleation-dependent tau filament formation. Understanding the kinetic roles of the inducer heparin and of rod-like protofibrils during amyloid fibril formation by tau protein. Resonance Raman spectroscopic measurements delineate the structural changes that occur during tau fibril formation.

Fracture and growth are competing forces determining the fate of conformers in tau fibril populations. Front Mol Neurosci. Nucleation-dependent conformational conversion of the YStop variant of human prion protein: structural clues for prion propagation. Structural polymorphism in amyloids. New insights from studies with YStop prion protein fibrils. Intermolecular alignment in YStop human prion protein amyloid fibrils probed by solid-state NMR spectroscopy. Acid-induced molten globule state of a prion protein.

Crucial role of strand 1-helix1-strand 2 segment. Oligomerization of the human prion protein proceeds via a molten globule intermediate. Singh J, Udgaonkar JB. The pathogenic mutation TA converts the prion protein into a molten globule-like conformation whose misfolding to oligomers but not to fibrils is drastically accelerated. Pathogenic mutations within the disordered palindromic region of the prion protein induce structure therein and accelerate the formation of misfolded oligomers.

Pathogenic mutations within the hydrophobic domain of the prion protein lead to the formation of protease-sensitive prion species with increased lethality. J Virol. Formation of critical oligomers is a key event during conformational transition of recombinant Syrian hamster prion protein. Dynamic equilibria between monomer and oligomeric misfolded states of the mammalian prion protein measured by 19 F NMR. Dissection of conformational conversion events during prion amyloid fibril formation using hydrogen exchange and mass spectrometry.

Structural effects of multiple pathogenic mutations suggest a model for the initiation of misfolding of the prion protein. N-terminal domain of prion protein directs its oligomeric association. The structural architecture of an infectious mammalian prion using electron cryomicroscopy.

PLoS Pathog. Ex vivo mammalian prions are formed of paired double helical prion protein fibrils. Open Biol. Amyloid fibrils of the HET-s — prion form a beta solenoid with a triangular hydrophobic core. Proteins have several layers of structure each of which is important in the process of protein folding. The first most basic level of this structure is the sequence of amino acids themselves. A novel sequence-based method based on the assumption that protein-protein interactions are more related to amino acids at the surface than those at the core.

The interactions of the amino acids will determine what the secondary and tertiary structure of the protein will be. The next layer in protein structure is the secondary structure. The secondary structure includes architectural structures that extend in one dimension. The tertiary structure is the next layer in protein structure. The description of globular protein structures as an ensemble of contiguous closed loops or tightened end fragments reveals fold elements crucial for the formation of stable structures and for navigating the very process of protein folding.

These interactions are important because they lead to the global structure and help create channels and binding sites for enzymes. The last layer of protein structure is the quaternary structure. The folding transition and the functional transitions between useful states are encoded in the linear sequence of amino acids, and a long- term goal of structural biology is to be able to predict both the structure and function of molecules from the information in the sequence.

Proteins are folded and held together by several forms of molecular interactions. The molecular interactions include the thermodynamic stability of the complex, the hydrophobic interactions and the disulfide bonds formed in the proteins.

The biggest factor in a proteins ability to fold is the thermodynamics of the structure. The interaction scheme includes the short-range propensity to form extended conformations, residue-dependent long-range contact potentials, and orientation-dependent hydrogen bonds. The use of energy diagrams and maps are key in finding out when the protein is in the most stable form possible.

The next type of interaction in protein folding is the hydrophobic interactions within the protein. The framework model and the hydrophobic collapse model represent two canonical descriptions of the protein folding process.

The first places primary reliance on the short-range interactions of secondary structure and the second assigns greater importance to the long-range interactions of tertiary structure. Globular proteins acquire distinct compact native con- formations in water as a result of the hydrophobic effect.

The hydrophobic interactions are found to affect time correlation functions in the vicinity of the native state even though they have no impact on same time characteristics of the structure fluctuations around the native state. The types of disulfide bonds are cysteine-cysteine linkage is a stable part of their final folded structure and those in which pairs of cysteines alternate between the reduced and oxidized states.

Proteins can miss function for several reasons. When a protein is miss folded it can lead to denaturation of the protein. Related Stories. Here, researchers describe a general Researchers have now identified some of These complex proteins are the result of evolution or design by scientists. Now scientists have discovered a new class of Biologists have studied how this process is triggered in mitochondria and identified a general alarm signal Scientists have developed a molecular probe that senses the state of the proteome -- the entire set of By watching their videos of this folding Abnormal activation of FoxM1 is a common feature of cancer cells



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