The Role of Non-Native Interactions in the Folding of Knotted Proteins

Biomolecules | Free Full-Text | The Role of Non-Native Interactions in the Folding of Knotted Proteins: Insights from...

Penn study shows how misfolded proteins are selected for disposal

Solution structure and dynamics of a de novo designed three-helix bundle protein | PNAS

Knots and Swelling in Protein Folding

A Two-Layer Learning Architecture for Multi-Class Protein Folds Classification: Medicine & Healthcare Book Chapter | IGI Global

Demonstration of a low-energy on-pathway intermediate in a fast-folding protein by kinetics, protein engineering, and...

Universal partitioning of the hierarchical fold network of 50-residue segments in proteins | BMC Structural Biology | Full Text

Sequence Similarity - 1CIQ: COMPLEX OF TWO FRAGMENTS OF CI2, RESIDUES 1-40 AND 41-64 Sequence Similarity Report Page

Protein Folding Triggered by Electron Transfer - CaltechAUTHORS

RCSB PDB - 1CIQ: COMPLEX OF TWO FRAGMENTS OF CI2, RESIDUES 1-40 AND 41-64 Macromolecule Annotations Page

The three-state model of Dunham et al. 1993 is among th | Open-i

Protein Folds Violate Evolutionary Expectations | Evolution News

post by Jess117

Protein-folding simulations sped up

The Best Arrangement To Make Your Minimalist Bedroom Design Looks So Attractive With a Wooden and Gray Accent - RooHome

Beware the Keeping Up With the Joneses Trap of a Minimalist Lifestyle

71+ Minimalist Aesthetic Macbook Pro Wallpaper Images - JEFAR.NET

The best minimalist wallet for modern men - fashionable and convenient! - Cool Men Style 2017

Protein folding

Striving For A More Simple/Minimalist Life Tribe - Mothering Forums

MINIMALISM

MINIMALIST Illuminating Serum

CiNii Articles - 垣内 雅彦

Protein Misfolding Diseases: Current and Emerging Principles by Marina Ramirez-Alvarado, Jeffery W. Kelly, Christopher M. -...

cond-mat.soft - Soft Condensed Matter: 1306.3850 (Changbong Hyeon et al.)

Aneuploidy-induced proteotoxic stress can be effectively tolerated without dosage compensation, genetic mutations, or stress...

Oxidative Stress and Proteostasis Network: Culprit and Casualty of Alzheimers-Like Neurodegeneration

A simple way to measure protein refolding rates in water

Prions and the potential transmissibility of protein misfolding diseases. - PubMed - NCBI

Characterization of purified myocilin: glaucoma as a protein misfolding disease - Raquel Lieberman

Mathematical model for fragmentation of bacterial inclusion bodies

PLOS Computational Biology: Trade-off between Positive and Negative Design of Protein Stability: From Lattice Models to Real...

TatD is a central component of a Tat translocon‐initiated quality control system for exported FeS proteins in Escherichia coli ...

[email protected]: Protein structure and interaction under environmental stress : from quality control recognition to...

Deutsches Krebsforschungszentrum

Probing the interface in a human co-chaperonin heptamer: residues disrupting oligomeric unfolded state identified | BMC...

Huntingtons Disease: Hot on the Trail of Misfolded Proteins Toxic Modus Operandi

José M. Barral, M.D., Ph.D. | The Pew Charitable Trusts

proteome zone: FEBS Letters issue on Protein Misfolding and Disease

Deglycosylated milin unfolds via inactive monomeric intermediates - DRO

Safe Review: ChubbSafes DuoGuard GO Model 40K Key Locking Eurograde Safe - Safe Options

Knot theory and proteins | Institute for Mathematics and its Applications

Department of clarification, Protein misfolding division

PAR-06-479: Targeting Diseases Caused by Protein Misfolding or Misprocessing (R01)

Jonathan S. Weissman, PhD Research Abstract | HHMI.org

The Protein Society : Protein Science

MyJournals.org - Science - Molecules, Vol. 25, Pages 251: Structural Disorder in High-Spin {CoII9WV6} (Core)-[Pyridine N...

Arizona universities join forces to contribute to COVID-19 modeling and simulation efforts | Graduate College

Protein Science

Protein Science

Tecan Journal | Protein Science & Mass Spec

Sanofi snaps up Protein Sciences for $650 million - PharmaTimes

protein folds - Everything2.com

Antievolution.org - Antievolution.org Discussion Board -Topic::Science Break

Antievolution.org - Antievolution.org Discussion Board -Topic::Science Break

Dead Time Lyrics - Inbred

A trick to fold proteins more quickly

N-cyclopropyl adenosine-5-carboxamide | Semantic Scholar

Novel motion capture-like technology for tracking how proteins fold into certain shape

Elastic Interactions Of Membrane Proteins | Science 2.0

Minimalist Sulfur Cavern Designs | CoolBoom

WYN Minimalist Wallet by WynLABS - Kickstarter

Minimalist Living Space Inspired by the Japanese Nakagin Capsule

Kayla - The Minimalist Pantry

In its native state, which of the following elem... - OpenStudy

Minimalist Cheer Holiday Cards | Paper Culture

Proteins may prevent dysfunction, disease by relaxing, study shows - Healthglu

Search: [fun] - [email protected]

A Post-Modernist California Is Born - latimes

Protein folding

Hydrophobic-polar protein folding model

Protein fold class

Metallo-beta-lactamase protein fold

Max Planck Research Unit for Enzymology of Protein Folding

Beta trefoil fold

List of Folding@home cores

Folding@home

Death fold

Rossmann fold

Jelly roll fold

Schellman loop

List of unsolved problems in biology

Max Planck Institute of Biochemistry

Aprotinin

Thioredoxin fold

Flavodoxin fold

Richard I. Morimoto

Bengt Nölting

Ribosome

Structural biology

Familial amyloid neuropathy

Molecular Operating Environment

Chaperone code

Anfinsen's dogma

Protein complex

List of unsolved problems in chemistry

Hydrogen bond

Protein

State switching

Phage display

PANO1

List of restriction enzyme cutting sites: Bst-Bv

Proto-oncogene tyrosine-protein kinase Src

2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase

Strømme syndrome

Caspase-activated DNase

NOL3

GANC

TENM3

ENTH domain

Metabolism

YqaJ protein domain

Genomic imprinting

Genome size

NXPH1

Equine anatomy

Denaturation midpoint

HSPA1B

Sparassis

TIMM10

Lewis Joel Greene

MiR-137

Diseases of poverty

Voltage-gated ion channel

PTBP1

Viroporin

Promoter (genetics)

FAM178B

Tetratricopeptide repeat protein 39B

Conformation8

• The amino-acid sequence (or primary structure ) of a protein predisposes it towards its native conformation or conformations. (bionity.com)
• We devised a new conformation search method, called Window Growth Evolutionary Algorithm (WGEA), for ab initio protein structure prediction. (iscb.org)
• Nelson explains that, as powerful as the AlphaFold algorithm is, it has not solved the protein-folding problem, if we take such a solution to mean "predicting the three-dimensional conformation of a protein strictly from its primary DNA sequence, ab initio . (evolutionnews.org)
• Compared with other chemical or physical denaturing agents, a unique feature of pressure is its ability to induce subtle changes in protein conformation, allowing the stabilization of partially folded states that are usually not significantly populated under more drastic conditions. (fiocruz.br)
• For FimA from Escherichia coli , it has been previously shown that the protein can also adopt a monomeric, self-complemented conformation in which the donor strand is inserted intramolecularly in the opposite orientation relative to that observed for FimA polymers. (jbc.org)
• Also, sometimes when I run docking from unbound components of the complex, I get this error message: ERROR: Conformation: fold_tree nres should match conformation nres. (rosettacommons.org)
• conformation nres: 628 fold_tree nres: 639 When I comment out the native complex structure, there is no more error. (rosettacommons.org)
• Native or wild-type quaternary protein structure is usually born from a single translated protein sequence with one ordered conformation with downstream protein interactions. (medscape.com)

Aggregation16

• Hartl showed that the antibiotic Geldenamycin affected the number of chaperones, helping to inhibit Huntington protein aggregation. (usc.edu)
• We highlight the fundamental similarity between these states and the amyloid structures responsible for many neurodegenerative diseases, and we discuss potential consequences for mechanisms of protein aggregation and intermolecular amyloid formation. (bath.ac.uk)
• The latter process often leads to protein aggregation and precipitation with the aggregates adopting either highly ordered (amyloid fibril) or disordered (amorphous) forms. (edu.au)
• Understanding the energetic and structural basis of protein folding in a physiological context may represent an important step toward the elucidation of protein misfolding and aggregation events that take place in several pathological states. (fiocruz.br)
• In particular, investigation of the structure and thermodynamic properties of partially folded intermediate states involved in productive folding or in misfolding/aggregation may provide insight into these processes and suggest novel approaches to prevent misfolding in living organisms. (fiocruz.br)
• In the past few years, hydrostatic pressure has been increasingly used as a thermodynamic variable in the study of both protein folding and misfolding/aggregation transitions. (fiocruz.br)
• Much of the recent work in this field has focused on the characterization of folding intermediates, because they seem to be involved in a variety of disease-causing protein misfolding and aggregation reactions. (fiocruz.br)
• Here, we review recent examples of the use of hydrostatic pressure as a tool to gain insight into the forces and energetics governing the productive folding or the misfolding and amyloid aggregation of proteins. (fiocruz.br)
• Dr Brockwell said: There are very few existing protein tests available to industry which actually examine how aggregation levels are related to manufacturing conditions. (leeds.ac.uk)
• Using the new device to gather evidence, researchers (Dr Amit Kumar and Mr Leon Willis, led by Professor Sheena Radford and Dr Brockwell) were able to calculate exactly the extent of the protein aggregation, creating a new evidence base for industry. (leeds.ac.uk)
• The team also found that aggregation in a range of proteins was diverse and was particularly damaging to therapeutic proteins such as biopharmaceutical antibodies under conditions similar to those found in standard manufacturing processes. (leeds.ac.uk)
• The results of the research, Inducing protein aggregation by extensional flow , are published in the Proceedings of the National Academy of Sciences journal. (leeds.ac.uk)
• a class of over 100 human diseases caused by the misfolding, aggregation, and accumulation of protein in specific cells leading to their dysfunction. (uchicago.edu)
• However, amyloid fibrils are different from the native states of their precursor proteins and therefore the adaptation of AlphaFold to study protein misfolding and aggregation, perhaps by predicting the structures of complex amyloid fibrils, might be better able to predict the effects of mutations that alter people's risk of developing amyloidosis. (mm713.org)
• Aggregation can lead to loss of the activity of the molecule, may lead to hypersensitivity reactions in the patient, and can make future doses of the medication ineffective if the patient develops antibodies against the active protein," he explains. (biopharminternational.com)
• Only 10% of amyloidosis deposits consist of components such as glycosaminoglycans (GAGs), apolipoprotein-E (apoE), and serum amyloid P-component (SAP), while nearly 90% of the deposits consist of amyloid fibrils that are formed by the aggregation of misfolded proteins. (medscape.com)

Sequences8

• Every two years, scores of teams from more than 20 countries blindly attempt to predict using computers the shape of a set of around 100 proteins from amino acid sequences alone. (freethoughtblogs.com)
• Shorter trajectories - 100-500 times shorter than equilibrium - led to errors due to "the peculiar behavior of the fast folding events that consist of atypical sequences of conformational transitions, not representative of the major folding pathways. (genomeweb.com)
• The reason, according to Nelson, is that while proteins, protein sequences, and protein folding promise to reveal much that is still mysterious in molecular biology, we now know that biological information involves far more than just an organism's proteome - that is, far more than the full suite of proteins expressed by an organism. (evolutionnews.org)
• The past few decades have seen an explosive growth in information about genomic sequences and the structures of the proteins they encode. (elsevier.com)
• DeepMind solved the notoriously difficult problem using a machine learning system called AlphaFold which has been trained on around 170,000 protein structures and other large databases of protein sequences. (acs.org.au)
• The ability to predict protein folding in three dimensions may result in the ability to predict which protein sequences are likely to form amyloid fibrils. (mm713.org)
• This strongly suggests functional reasons for the amino acid sequences of human and ape proteins, and shows their similarities can be explained as being due to functional requirements. (evolutionnews.org)
• What has concerned some scientists recently however is that there are proteins with similar shapes but the controlling nucleotide sequences are very different. (create.ab.ca)

Intrinsically disordered proteins1

• A few areas of interest are - regulation of transcription factors, DNA repair mechanisms, protein folding and mis-folding, intrinsically disordered proteins, enzyme catalysis and protein engineering. (iitkgp.ac.in)

Prion7

• [3] Failure to fold into the intended shape usually produces inactive proteins with different properties (details found under prion ). (bionity.com)
• The mis-folded prion protein forms protein aggregates in cells, and is able to cause healthy versions of the protein to become mis-folded as well. (harvard.edu)
• CJD is caused by a protein called a prion. (medlineplus.gov)
• A prion causes normal proteins to fold abnormally. (medlineplus.gov)
• The term "prions" refers to abnormal, pathogenic agents that are transmissible and are able to induce abnormal folding of specific normal cellular proteins called prion proteins that are found most abundantly in the brain. (cdc.gov)
• The functions of these normal prion proteins are still not completely understood. (cdc.gov)
• The abnormal folding of the prion proteins leads to brain damage and the characteristic signs and symptoms of the disease. (cdc.gov)

Molecular chaperones4

• The molecular chaperones are central mediators of protein homeostasis. (jbc.org)
• While these macromolecules may be regarded as "folding themselves", the mechanism depends equally on the characteristics of the cytosol, including the nature of the primary solvent (water or lipid ), the concentration of salts , the temperature, and molecular chaperones . (bionity.com)
• This event is prevented by small Heat Shock Proteins (sHSPs) acting as molecular chaperones. (iisc.ac.in)
• Small heat shock proteins (sHSPs) are a ubiquitous family of molecular chaperones that play a vital role in maintaining protein homeostasis in cells. (iisc.ac.in)

Chains of amino acids2

• Proteins are made of long chains of amino acids. (usc.edu)
• They are large complex molecules, made up of chains of amino acids, and what a protein does largely depends on its unique 3D structure. (mm713.org)

Heat shock pr2

• The core chaperones, such as the heat shock proteins Hsp60, Hsp70, and Hsp90, are widely expressed in most tissues, yet there is growing evidence that the PPIs among them may be re-wired in disease conditions. (jbc.org)
• In eukaryotic organisms chaperones are known as heat shock proteins . (bionity.com)

Structures15

• Often folding involves first the establishment of regular secondary and supersecondary structures, particularly alpha helices and beta sheets , and afterwards tertiary structure . (bionity.com)
• The regular alpha helix and beta sheet structures fold rapidly because they are stabilized by intramolecular hydrogen bonds, as was first characterized by Linus Pauling . (bionity.com)
• In the 1940s, Linus Pauling and Robert Corey elucidated the a-helix and the b-sheet, which are considered the two fundamental building blocks of all protein secondary structures. (the-scientist.com)
• In contrast, a conventional Monte-Carlo method, which is like WGEA but which does not have the window growth feature, give structures with RMS values greater than 4 for the same set of proteins. (iscb.org)
• At the same time, the 3-D structures are worked out in the lab by biologists using traditional techniques like X-ray crystallography and NMR spectroscopy, which determine the location of each atom relative to each other in the protein molecule. (freethoughtblogs.com)
• A team of scientists from Casp (the Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction) then compares these predictions with 3-D structures solved using experimental methods. (freethoughtblogs.com)
• The protein folding problem refers to the high level of complexity involved in the way proteins go from being simple strings of amino acids to folded 3D structures inside cells. (acs.org.au)
• Parvalbumin, a protein found in great quantities in several different fish species, has been shown to help prevent the formation of certain protein structures closely associated with Parkinson's disease. (neurosciencenews.com)
• What the Chalmers researchers have now discovered, is that parvalbumin can form amyloid structures that bind together with the alpha-synuclein protein. (neurosciencenews.com)
• In the manual for protein docking, there is another application for preparing structures for docking: docking prepack protocol. (rosettacommons.org)
• This prepack protocol can generate input structures from bound protein-protein complex. (rosettacommons.org)
• So how can I generate input structures from unbound protein components (for example, if protein A and B form a complex, and I have the structures for A alone and B alone)? (rosettacommons.org)
• You can now dive deep into your proteins, cavities, and binding sites using crystal structures and state-of-the-art AI models from OpenFold (powered by NVIDIA's BioNeMo service), DeepMind`s AlphaFold and ESMFold by Meta. (pymolwiki.org)
• Catalophore™ Cavities can be calculated for molecules loaded in PyMOL * Predict protein structures within seconds for any protein sequence using [https://www.nvidia.com/en-us/gpu-cloud/bionemo OpenFold] by NVIDIA [https://www.nvidia.com/en-us/gpu-cloud/bionemo BioNeMo] (coming soon! (pymolwiki.org)
• The structures show that the overall fold of Sbi00515 is nearly identical to those of both ADC and MppR. (nih.gov)

Secretory proteins2

• This leads to a dysregulation of triglyceride and free fatty acid levels, as well as a dysregulation of specific adipocyte-derived secretory proteins, a group of proteins that we refer to as adipokines. (diabetesjournals.org)
• Additional proteins have joined this exclusive club of adipocyte-specific secretory proteins since then, including adipokines such as resistin ( 11 , 12 ) and acylation-stimulating protein ( 13 ), as well as the recently described visfatin ( 14 , 15 ) and retinol-binding protein-4 ( 16 ). (diabetesjournals.org)

Ribosome6

• The process of folding in vivo often begins co-translationally , so that the N-terminus of the protein begins to fold while the C-terminal portion of the protein is still being synthesized by the ribosome . (bionity.com)
• It is the process by which proteins acquire their functional, preordained, three-dimensional structure after they emerge, as linear polymers of amino acids, from the ribosome. (the-scientist.com)
• Most proteins start folding within a minute, at most, after leaving the ribosome. (the-scientist.com)
• The 2020 Annual Meeting on Protein Folding on the Ribosome will be held at Johns Hopkins University in Baltimore, MD on December 11-13, 2020. (elsevier.com)
• The E. coli ribosome exit tunnel can accommodate small folded proteins, while larger ones fold outside. (elifesciences.org)
• At longer linker lengths, F and f FL ≈ 0 because the domain is already folded when the ribosome reaches the end of the AP. (elifesciences.org)

Molecules11

• Most folded proteins have a hydrophobic core in which side chain packing stabilizes the folded state, and charged or polar side chains on the solvent-exposed surface where they interact with surrounding water molecules. (bionity.com)
• For the most part, scientists have been able to study many identical molecules folding together en masse . (bionity.com)
• During his lecture, Hartl gave some history of his collaboration with Horwich, beginning with their work in 1988 that showed the basic role of chaperone molecules in protein folding. (usc.edu)
• He described how the chaperonins GroEL and GroES create a safe cage structure that allows single-protein molecules to fold. (usc.edu)
• Model tasks involve characterizing the distinct structural fluctuations of the protein bound to various drug molecules, as well as efficient generation of protein conformations that can serve as an complement of a molecular simulation engine. (arxiv.org)
• As such, the ability of some molecules, for example, the small heat-shock family of molecular chaperone proteins, to inhibit fibril formation is of interest due to their therapeutic potential. (edu.au)
• Usually, scientists create images of proteins by taking millions of snaps of different molecules. (gizmodo.com)
• This process which can be highly damaging to bio-molecules, such as protein-based biopharmaceutical therapeutics, dissolved in the fluid, is known as extensional flow and is occurs when the fluid rapidly accelerates its movement. (leeds.ac.uk)
• To characterize the primary structure information of the protein molecules more comprehensively, we considered sequence length, residue components with different scales, k -space features for pair residues, and geostatistics association features among different locations of the residues substituted with corresponding physical-chemical properties. (pku.edu.cn)
• While storage and release of lipids are major functions of adipocytes, the adipocyte also uses specific lipid molecules for intracellular signaling and uses a host of protein factors to communicate with essentially every organ system in the body. (diabetesjournals.org)
• This transcription factor governs the expression of target genes that are involved in encoding cytokines, chemokines, growth factors, cell adhesion molecules, and acute-phase proteins that regulate inflammation, cell proliferation, and apoptosis. (cdc.gov)

Aggregates1

• Amyloidosis results from the accumulation of pathogenic amyloids-most of which are aggregates of misfolded proteins-in a variety of tissues. (medscape.com)

Gastric folds2

• Ménétrier disease is characterized by large gastric folds with excess mucus production and resultant protein loss. (medscape.com)
• A rare gastrooesophageal disease characterised by diffusely enlarged gastric folds, excessive mucus secretion, normal serum protein and gastric TGF-alpha levels. (cdc.gov)

Prediction8

• Co-founder of the biennial Critical Assessment of protein Structure Prediction (CASP) experiment, Professor John Moult, said he was happy to see DeepMind offer a solution to this long-standing biological challenge. (acs.org.au)
• In this paper, a model based on genetic algorithms for protein folding prediction is proposed. (duartetorres.com)
• Folding rate prediction plays an important role in clarifying the protein folding mechanism. (pku.edu.cn)
• 1999. " Ab Initio Protein Structure Prediction With Molego " . (uni-heidelberg.de)
• 1998. " Implementing Genetic Algorithms With Sterical Constraints For Protein Structure Prediction " . (uni-heidelberg.de)
• 2000. " Protein Structure Prediction Using Combinatorial Optimization " . (uni-heidelberg.de)
• 1998. " Protein Structure Prediction With Combinatorial Optimization " . (uni-heidelberg.de)
• In Third Community Wide Experiment On The Critical Assessment Of Techniques For Protein Structure Prediction, Casp3 , 77. (uni-heidelberg.de)

Demonstrating stability1

• We find that the protein shows a surprising resilience toward extremes of pH, demonstrating stability and function (cellulose binding) in the pH range from 2 to 11. (uni-koeln.de)

Polypeptide5

• Protein folding is the physical process by which a polypeptide folds into its characteristic three-dimensional structure . (bionity.com)
• [1] Each protein begins as a polypeptide , translated from a sequence of mRNA as a linear chain of amino acids. (bionity.com)
• The focus of this meeting will be on emergent topics, including nascent polypeptide chain structure and folding, regulation of translation, and nascent chain targeting and translocation to membranes. (elsevier.com)
• They are classified as integral, peripheral membrane proteins and polypeptide toxins. (iisc.ac.in)
• The specific sequence of amino acids determines the shape the polypeptide will take, during protein folding, and the function of the protein. (lecturio.com)

Stability of proteins2

• Excipients not only affect the stability of proteins and other biologics, they also determine the appropriate operating parameters for the lyophilization process. (biopharminternational.com)
• QSOX1 participates in the folding and stability of proteins and thus could regulate the biological activity of its substrates in the secretory pathway and/or outside the cell. (inserm.fr)

Processes13

• Together, these PPIs form the backbone of a network that ensures proper vigilance over the processes of protein folding, trafficking, quality control, and degradation. (jbc.org)
• Developing an understanding of protein misfolding processes presents a crucial challenge for unlocking the mysteries of human disease. (bath.ac.uk)
• This mini-review focuses on the processes and consequences of protein folding and misfolding. (edu.au)
• Biopharma and food businesses working with proteins now have access to better information about how a type of fluid flow used in manufacturing processes can affect the quality of their products. (leeds.ac.uk)
• Dr David Brockwell from the University of Leeds Astbury Centre for Structural Molecular Biology said while many tests existed to assess the effects of changes in temperature or pH on protein stability, this test gauged directly the effects of fluid flows used in manufacturing processes. (leeds.ac.uk)
• What we now have is a much more accurate way of predicting which proteins can be used in biopharmaceutical drug development and how processes could also be changed to improve their quality. (leeds.ac.uk)
• The evidence from the new device means the researchers and Medimmune can now demonstrate maximal levels of extensional flow which manufacturers could use for different processes, without damaging proteins. (leeds.ac.uk)
• As a result, proteins drive many of the reactions and processes which are vital to the life of the cell. (harvard.edu)
• Theoretically, the possibilities include (1) a primary T-cell mediated autoimmune response causing muscle damage, (2) a primary degenerative process involving abnormal protein processing leading to a secondary inflammatory response, and (3) separate and independent immune and degenerative processes caused by an external trigger. (medscape.com)
• Processes involved in the formation of TERTIARY PROTEIN STRUCTURE . (bvsalud.org)
• The turnover of proteins is one of the cell's most essential processes and is necessary for responding to external stimuli and for maintaining homeostasis . (cdc.gov)
• By cataloguing the molecular processes by which cells maintain and modify protein levels, proteomic studies offer another dimension of information that may help advance our understanding of health and disease. (cdc.gov)
• Polymorphisms that slightly vary native peptides or inflammatory processes set the stage for abnormal protein folding and amyloid fibril deposition. (medscape.com)

Diseases6

• Several neurodegenerative and other diseases are believed to result from the accumulation of misfolded (incorrectly folded) proteins. (bionity.com)
• Improperly or incompletely folded proteins can lead to organ malfunction and neurodegenerative diseases. (usc.edu)
• In each of these diseases a different protein forms fibrils, yet the fibrils formed have a very similar structure. (edu.au)
• Improper folding of proteins may cause serious diseases. (harvard.edu)
• For diseases which originate with misfolded proteins, such as amyloidosis, "investigators have been doing this exercise by 'brute force' until now," according to Dr. Angela Dispenzieri from the Mayo Clinic. (mm713.org)
• It is clear that DeepMind will provide important basic understanding of the folding process and will significantly benefit those amyloidosis diseases that involve secreted, folded proteins, such as light chain (AL), and Transthyretin (ATTR) amyloidosis. (mm713.org)

Strings of amino acids1

• Protein are linear strings of amino acids. (freethoughtblogs.com)

Membrane proteins2

• Successes in structural studies of membrane proteins deserve to be celebrated. (nature.com)
• Membrane proteins roughly constitute 30% of open reading frames in a genome and form 70% of current drug targets. (iisc.ac.in)

20201

• 2020. Structurally distinct telomere-binding proteins in Ustilago maydis execute non-overlapping functions in telomere replication, recombination, and protection. . (cornell.edu)

Subunit2

• Up to 3000 copies of FimA assemble to the helical pilus rod through a mechanism termed donor strand complementation, in which the incomplete immunoglobulin-like fold of each FimA subunit is complemented by the N-terminal extension (Nte) of the next subunit. (jbc.org)
• 2011. Structural bases of dimerization of yeast telomere protein Cdc13 and its interaction with the catalytic subunit of DNA polymerase α. . (cornell.edu)

Function20

• For many proteins the correct three dimensional structure is essential to function. (bionity.com)
• When coordinate root mean square (cRMS) deviation from the experimental structure is used as the energy function, WGEA folds these proteins to an average accuracy of 1.5 for a-helical proteins, 2 for the a/b class proteins, and 2.8 for the b-class proteins. (iscb.org)
• The whole decentralized system is used to make a protein that will function as an antibody, able to fight the virus. (guru3d.com)
• Nascent protein folding, targeting and quality control are key to ensuring proper cellular function. (elsevier.com)
• Thus, the meeting will serve as a platform for scientists to continue to advance understanding of different facets of protein biogenesis and how they enable cellular function and complexity. (elsevier.com)
• Charges are considered an integral part of protein structure and function, enhancing solubility and providing specificity in molecular interactions. (uni-koeln.de)
• We wished to investigate whether charged amino acids are indeed required for protein biogenesis and whether a protein completely free of titratable side chains can maintain solubility, stability, and function. (uni-koeln.de)
• To further deprive this protein of charges, we removed the N-terminal charge by acetylation and studied the protein at pH 2, where the C-terminus is effectively protonated, Under these conditions, the protein retains its function and proved to be both soluble and have a reversible folding-unfolding transition. (uni-koeln.de)
• Abstract: Protein fold recognition plays an important role in computational protein analysis since it can determine protein function whose structure is unknown. (thesai.org)
• In the fold recognition phase, unknown protein folds are predicted via a proposed testing function. (thesai.org)
• Proteins function as enzymes which catalyze desirable chemical reactions, are integral structural components of the cell, and provide biochemical signals and receptors for the cell. (harvard.edu)
• This affects other proteins' ability to function. (medlineplus.gov)
• The switch from electron transfer to peroxidase function requires partial unfolding of the protein upon binding of CL, whose specific features combine negative charges of the two phosphate groups with four hydrophobic fatty acid residues. (cdc.gov)
• Nanowerk News ) Researchers at the National Institute of Standards and Technology (NIST) have developed a new statistical tool that they have used to predict protein function. (nanowerk.com)
• Since the 1960s, biologists have understood that the shape of a protein is essential to its function. (create.ab.ca)
• Proteins can unfold during heat and other types of stress and tend to aggregate with subsequent loss of function. (iisc.ac.in)
• 2000. " Secondary Structure And Function Based Protein Fold Recognition " . (uni-heidelberg.de)
• New insights into the genome have led to the emergence of proteomics , the study of the structure and function of an individual's entire set of expressed proteins. (cdc.gov)
• The life cycle of a protein starts with a blueprint transcribed from a gene, followed by folding, which translates the blueprint to a three-dimensional structure that allows it to carry out its biological function, and ends with degradation. (cdc.gov)
• Many mechanisms of protein function contribute to amyloidogenesis, including "nonphysiologic proteolysis, defective or absent physiologic proteolysis, mutations involving changes in thermodynamic or kinetic properties, and pathways that are yet to be defined. (medscape.com)

Unfold3

• Horwich described how proteins must unfold to enter cell mitochondria and then refold once inside. (usc.edu)
• Proteins naturally fold into specific shapes in order to operate correctly, but extensional flow can cause them to stretch and unfold, making them less useful. (leeds.ac.uk)
• Once they begin to unfold, proteins stick together, or aggregate, which can block sensitive factory equipment and decrease the effectiveness of the medicines they are contained in, and can even pose a danger to people. (leeds.ac.uk)

Small proteins2

• Some small proteins can acquire the native state. (the-scientist.com)
• This procedure was tested on off-lattice, discrete state models of a set of small proteins. (iscb.org)

Already folded1

• Formation of quaternary structure usually involves the "assembly" or "coassembly" of subunits that have already folded. (bionity.com)

Substances1

• Because the conditions during freezing and drying are different, the stresses on biologic drug substances are different, and combinations of excipients are often required to provide the protection and stabilization required for a given protein, monoclonal antibody, etc. (biopharminternational.com)

Nascent chain1

• 0 because the domain pulls on the nascent chain as it folds. (elifesciences.org)

Abnormal protein1

• The disruption of protein homeostasis due to chronic stress responses at the endoplasmic reticulum (ER) and the accumulation of abnormal protein inclusions are extensively described in ALS mouse models and patient-derived tissue. (harvard.edu)

Shapes3

• The program then "learns" using information on the 3-D shapes of known proteins held in a worldwide database. (freethoughtblogs.com)
• The chains fold to form specific shapes that help the proteins carry out their specific functions. (usc.edu)
• Figuring out what shapes proteins fold into is known as the "protein folding problem. (mm713.org)

Fibrils2

• Amyloid fibrils are protein polymers comprising identical monomer units (homopolymers). (medscape.com)
• [ 5 ] In humans, about 23 different unrelated proteins are known to form amyloid fibrils in vivo. (medscape.com)

Amyloid formation1

• One of the hallmarks of Parkinson's disease is amyloid formation of a particular human protein, called alpha-synuclein. (neurosciencenews.com)

Sequence of amino acids2

• contribs ) (New page: == Definition == '''Protein folding''' is the process by which a large sequence of amino acids is arranged physically into the complex structure of a functioning protein. (harvard.edu)
• Many studies show that the sequence of amino acids is vital to protein functionality. (evolutionnews.org)

Spike5

• SARS-CoV-2 Spike protein, obtained from computationally expensive molecular simulations. (arxiv.org)
• understanding how changes in the DNA can alter this spike protein might help epidemiologists predict the future of the pandemic. (nanowerk.com)
• Now he is working on a number of important proteins in real life, including the light-gated chloride-pumping rhodopsin and the human receptor protein ACE2 in conjugation with the SARS-CoV-2 viral spike protein. (edu.hk)
• The Long-haul and vaccine adverse event knowledge-base is updated daily and provides the latest science-based research findings concerning the chronic conditions that long-haul sufferers experience and the research findings of basic and clinical researchers who are working to understand the causes of the damage that appear throughout the body from the virus and the spike proteins that are responsible for them. (cov19longhaulfoundation.org)
• The ChAdOx1-S [recombinant] vaccine uses a DNA adenovirus vector to elicit antibodies to the SARS-CoV-2 spike protein. (who.int)

Cellular2

• In class I mutations, premature termination codons prevent the production of any functional protein, resulting in severe CF. Therapies targeting class I mutations aim to enable the normal cellular mechanism to read through the mutation, potentially restoring the production of the CFTR protein. (bvsalud.org)
• When a cell is perturbed, it responds by altering expressing levels of specific proteins and adjusting cellular functions in response to the new environmental stimuli. (cdc.gov)

Residues10

• Protein folding may involve covalent bonding in the form of disulfide bridges formed between two cysteine residues or the formation of metal clusters. (bionity.com)
• Excluding knots formed by post-translational crosslinking, the few proteins considered to be knotted form simple trefoil knots with one end of the chain extending through a loop by only a few residues, ten in the 'best' example. (nih.gov)
• It characterizes knots in proteins by the number of residues that must be removed from each end to abolish the knot. (nih.gov)
• The domain to be studied is placed L residues upstream of the critical proline at the C-terminal end of the 17-residue long arrest peptide (AP) from the E. coli SecM protein. (elifesciences.org)
• As a model, we used a cellulose-binding domain from Cellulomonas fimi, which, among proteins of more than 100 amino acids, presently is the least charged in the Protein Data Bank, with a total of only four titratable residues. (uni-koeln.de)
• To ask whether the four charged residues present were required for these properties of this protein, we altered them to nontitratable ones. (uni-koeln.de)
• By further analyzing the effects of each retained descriptor on protein folding rates, the results showed that the protein folding rate might be closely related to the sequence length, the features associated with the medium-and short-range, the triplet residues component features, etc. (pku.edu.cn)
• Based on protein dock, I assume I can do the same (get rid of the extra residues in whichever PDB is larger, or re-do the earlier steps for the smaller PDB to get them back into the larger PDB) to make use of the native pdb for RMSD calculations, right? (rosettacommons.org)
• In the proposed "zinc finger" DNA-binding motif, each repeat unit binds a zinc metal ion through invariant Cys and His residues and this drives the folding of each 30-residue unit into an independent nucleic acid-binding domain. (embl.de)
• Proteins are large biomolecules consisting of one or more long chains of amino acid residues. (iisc.ac.in)

Transition6

• Their astonishing result is that this quantum transition model fits the folding curves of 15 different proteins and even explains the difference in folding and unfolding rates of the same proteins. (kurzweilai.net)
• Transition path times with applications to protein folding and tunneling times. (uci.edu)
• Recent experimental measurements of the transition path time distributions of proteins moving from the folded to the unfolded state and vice versa, presented the theory with challenges. (uci.edu)
• Struggling with the concept of transition path times distributions for proteins naturally led to the question of what is the quantum analog and what can we learn from the same in the quantum mechanical context. (uci.edu)
• 2] R. Dutta and E. Pollak, What can we learn from transition path time distributions for protein folding and unfolding? (uci.edu)
• The protein folding is viewed from conformational quantum transition and the folding rate is calculated. (dspace.org)

Computational4

• Distributed computing - often touted as a breakthrough for the computational demands of protein-folding simulation - may not be as effective a solution as originally thought, according to several recent peer-reviewed papers. (genomeweb.com)
• Computational methods have been applied to determine a protein's fold by assembling information from its structural, physicochemical and/or evolutionary properties. (usp.ac.fj)
• This computational work represents a stunning advance on the protein-folding problem, a 50-year-old grand challenge in biology. (mm713.org)
• By means of a computational simulator based on the systemic diagramming, we identifid host protein recycling and folded-protein synthesis as possible new leverage points. (bvsalud.org)

Hydrophobic2

• It is generally accepted that minimizing the number of hydrophobic sidechains exposed to water is the principal driving force behind the folding process, [5] although a recent theory has been proposed which reassesses the contributions made by hydrogen bonding. (bionity.com)
• Sections with polar chemical groups will tend toward the outside of the protein, while groups with hydrophobic side chains are often found in the centre of the macromolecule where they are less likely to interact with water. (harvard.edu)

Functional2

• To the best of our knowledge, this is the first time a soluble, functional protein with no titratable side chains has been produced. (uni-koeln.de)
• The "protein folding problem" that DeepMind's AlphaFold is designed to solve is predicting the native, functional state of a protein from just its amino acid sequence. (mm713.org)

Temperature4

• Liaofu Luo at the Inner Mongolia University and Jun Lu at the Inner Mongolia University of Technology, both in China, have developed a mathematical model for how protein folding depends on temperature, and have derived equations that describe how the rate of " quantum folding " would change with temperature. (kurzweilai.net)
• Protein folding is highly dependent on the external factors such as the solvent, concentration of salts, and temperature. (harvard.edu)
• Lyophilization subjects a protein to conditions such as freezing, temperature ramps, vacuum, and dehydration, all of which can disrupt the fragile protein structure leading to loss of activity, according to Anjali Joshi, director of formulation development with Recipharm. (biopharminternational.com)
• The thermophilic methyltransferase M.TaqI is particularly suited to label DNA origami during folding because of two reasons: 1 - Its optimal working temperature lies between 50 °C and 65 °C, which is also the temperature range in which DNA origami folds. (rsc.org)

Subunits1

• Proteins Proteins Linear polypeptides that are synthesized on ribosomes and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. (lecturio.com)

Kinetics1

• We now performed the kinetics of folding of ABSS in urea and GdmCl at pH 2 and 7. (uzh.ch)

Synthesis1

• It will fold spontaneously during or after synthesis . (bionity.com)

Serum2

• This action results in reduced TTR protein levels in serum and tissue. (medscape.com)
• These include α1 acid glycoprotein, serum amyloid A, the C-reactive protein homolog pentraxin-3, the lipocalin 24p3, and a host of cytokines ( 17 ). (diabetesjournals.org)

Antibodies2

• Most serologic assays for flaviviruses measure antibodies binding to viral-envelope glycoprotein (E protein) because this antigen is a major target of human antibodies. (cdc.gov)
• We previously described a serologic assay using domain III of the ZIKV E protein (EDIII) to detect ZIKV type-specific antibodies among persons in areas with DENV and ZIKV cocirculation ( 19 ). (cdc.gov)

Globular2

• [7] A well studied example is the bacterial GroEL system, which assists in the folding of globular proteins . (bionity.com)
• Repeat proteins have a non-globular modular architecture acting as a scaffold for protein-protein interactions. (uzh.ch)

Conformations2

• It searches conformations using many small windows along the sequence of the protein, then the window size is gradually increased until it reaches the length of the whole protein. (iscb.org)
• Here we report the discovery of a family of self-constructing cyclic macromolecules with stable folded conformations of low symmetry, which include some with a prime number (13, 17 and 23) of units, despite being formed from a single component. (nature.com)

Structural4

• SCOPe: Structural Classification of Proteins - extended. (berkeley.edu)
• This work focuses on learning a generative neural network on a structural ensemble of a drug-target protein, e.g. (arxiv.org)
• Results show that our geometric learning-based method enjoys both accuracy and efficiency for generating complex structural variations, charting the path toward scalable and improved approaches for analyzing and enhancing high-cost simulations of drug-target proteins. (arxiv.org)
• We show that binding of the rotavirus-encoded non-structural protein NSP2 to viral ssRNAs results in the remodeling of RNA, which is conducive to formation of stable inter-segment contacts. (cipsm.de)

Dynamics5

• At issue is the way the distributed approach splits up the protein folding problem: A single molecular dynamics simulation on the time scale of tens of microseconds would take thousands of years of CPU time, so distributed projects perform tens of thousands of very short simulations, on the scale of tens of nanoseconds, via screen-saver programs on PCs spread across the globe. (genomeweb.com)
• We find that a 29-residue zinc-finger domain normally folding close to the uL23 loop folds deeper in the tunnel in uL23 Δloop ribosomes, while two ~ 100 residue proteins normally folding close to the uL24 loop near the tunnel exit port fold at deeper locations in uL24 Δloop ribosomes, in good agreement with results obtained by coarse-grained molecular dynamics simulations. (elifesciences.org)
• In this article, we present our observations of β-sheet-rich misfolded states on a number of protein dynamical landscapes investigated through molecular dynamics simulation and Markov state models. (bath.ac.uk)
• We employ a nonequilibrium statistical mechanical theory to identify the glassy states in a protein's dynamics, and we discuss the nonnative, β-sheet-rich states that play a distinct role in the slowest dynamics within seven protein folding systems. (bath.ac.uk)
• It is demonstrated that the conformational dynamics gives deep insights into the folding mechanism and provides a useful tool for analyzing and explaining experimental facts on the rate of protein folding. (dspace.org)

Gene1

• BACKGROUND: Cystic fibrosis (CF) is a common, life-shortening, genetic disorder in populations of Northern European descent caused by the mutation of a single gene that codes for the production of the cystic fibrosis transmembrane conductance regulator (CFTR) protein. (bvsalud.org)

Correctly2

• If the protein is not completely folded, it will be recaptured and processed again until it folds correctly. (usc.edu)
• A second one is an observation that when analyzed correctly, the measured distributions reveal long-time tails which may be identified with a long-lived intermediate, between the folded and unfolded states [2]. (uci.edu)

Disease5

• Here, we report the interaction between the human Hsp70 isoform heat shock cognate 71-kDa protein (Hsc70 or HSPA8) and peptides derived from the microtubule-associated protein Tau, which is linked to Alzheimer's disease. (jbc.org)
• Correct folding of proteins can make the difference between health and disease, according to researchers F. Ulrich Hartl of the Max Planck Institute of Biochemistry and Arthur Horwich of Yale University. (usc.edu)
• Working with Huntington's disease proteins, Hartl also found that disease occurs if there are not enough chaperonins to deal with the number of unfolded proteins. (usc.edu)
• Massive molecular simulations of drug-target proteins have been used as a tool to understand disease mechanism and develop therapeutics. (arxiv.org)
• Patients with Ménétrier disease may present with protein-losing enteropathy . (medscape.com)

AlphaFold3

• In the latest round of the challenge, Casp-14, AlphaFold determined the shape of around two thirds of the proteins with accuracy comparable to laboratory experiments. (freethoughtblogs.com)
• The AlphaFold system can take an amino acid sequence and output a highly accurate folded protein. (acs.org.au)
• In a major scientific breakthrough, DeepMind's AI system AlphaFold has been recognized as a solution to this grandest of all biological problems - the "protein folding problem. (mm713.org)

Residue1

• A 23-residue long stretch of the E. coli LepB protein is attached downstream of the AP, allowing us to separate the arrested ( A ) and full-length (FL) products by SDS-PAGE after translation. (elifesciences.org)

Intermediates2

• The folding of the designed ankyrin repeat obeys a two-state model at 5°C, while equilibrium intermediates populate at higher temperatures. (uzh.ch)
• Under both conditions the major disulfide folding pathway of HcpB involves only native disulfide intermediates. (uzh.ch)