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Categories of protein tertiary structure
molecular biology, protein fold classes are broad categories of protein tertiary structure topology. They describe groups of proteins that share similar
Protein_fold_class
Change of a linear protein chain to a 3D structure
Protein folding is the physical process by which a protein, after synthesis by a ribosome as a linear chain of amino acids, changes from an unstable random
Protein_folding
Biological database of proteins
a protein. For simple proteins, it can be the entire protein. The broadest groups on SCOP version 1.75 are the protein fold classes. These classes group
Structural Classification of Proteins database
Structural_Classification_of_Proteins_database
Artificial intelligence program by DeepMind
AlphaFold is an artificial intelligence (AI) program developed by DeepMind, a subsidiary of Alphabet, which performs predictions of protein structure.
AlphaFold
Grouping of proteins
the fold is the fold class, which describes a rough topology of the protein (e.g. all-α, all-β, α+β, α/β). Superfamilies of proteins are identified using
Protein_superfamily
Spherical, water-soluble type of protein
proteins. There are multiple fold classes of globular proteins, since there are many different architectures that can fold into a roughly spherical shape
Globular_protein
Self-stable region of a protein's chain that folds independently from the rest
In molecular biology, a protein domain is a region of a protein's polypeptide chain that is self-stabilizing and folds independently from the rest. Each
Protein_domain
Type of biological prediction
predict protein folding and thus protein structure, for example, Itasser, and AlphaFold. AlphaFold was one of the first AIs to predict protein structures.
Protein_structure_prediction
Biomolecule consisting of chains of amino acid residues
protein folding into a specific 3D structure that determines its activity. A linear chain of amino acid residues is called a polypeptide. A protein contains
Protein
Family of heat shock proteins
a family of heat shock proteins that assist in the folding of newly synthesized proteins and refolding of misfolded proteins during stressful conditions
Chaperonin
Superfamily of oxygen-transporting globular proteins
heme-containing globular proteins, involved in binding and/or transporting oxygen. These proteins all incorporate the globin fold, a series of eight alpha
Globin
Class of enzymes
are proteins that assist the conformational folding or unfolding of proteins or macromolecular protein complexes. There are a number of classes of molecular
Chaperone_(protein)
Small structural protein motif found mostly in transcriptional proteins
finger is a small protein structural motif that is characterized by the coordination of one or more zinc ions (Zn2+) which stabilize the fold. The term zinc
Zinc_finger
Type of cellular stress response
because proteins are the main functional units of the cell. Many proteins take on a defined configuration in a process known as protein folding in order
Heat_shock_response
Type of beta barrel protein domain structure
The jelly roll or Swiss roll fold is a protein fold or supersecondary structure composed of eight beta strands arranged in two four-stranded sheets. The
Jelly_roll_fold
Predicting 3D protein structure from its sequence
methods have a reasonable probability of predicting the folds of small, single-domain proteins within 1.5 angstroms over the entire structure. De novo
De novo protein structure prediction
De_novo_protein_structure_prediction
Three-dimensional arrangement of atoms in an amino acid-chain molecule
identified as a peptide, rather than a protein. To be able to perform their biological function, proteins fold into one or more specific spatial conformations
Protein_structure
General three-dimensional form of local segments of proteins
elements typically spontaneously form as an intermediate before the protein folds into its three dimensional tertiary structure. Secondary structure is
Protein_secondary_structure
helix/beta sheet proteins. While most proteins adopt a single stable fold, a few proteins can rapidly interconvert between one or more folds. These are referred
List_of_proteins
Protein fold class, typically
Small proteins are a diverse fold class of proteins (usually <100 amino acids long). Their tertiary structure is usually maintained by disulphide bridges
Small_protein
Type of protein fold
The thioredoxin fold is a protein fold common to enzymes that catalyze disulfide bond formation and isomerization. The fold is named for the canonical
Thioredoxin_fold
Protein fold
enzymes adopting this fold. Further, five of seven enzyme commission (EC) enzyme classes include TIM barrel proteins. The TIM barrel fold is evolutionarily
TIM_barrel
Class of proteins
Membrane fusion proteins (not to be confused with chimeric or fusion proteins) are proteins that cause fusion of biological membranes. Membrane fusion
Membrane_fusion_protein
Protein of the immune system
help of an MHC class I protein. Because MHC class I molecules present peptides derived from cytosolic proteins, the pathway of MHC class I presentation
MHC_class_I
Protein that exhibits bright green fluorescence when exposed to ultraviolet light
unintended protein product, using the +2 frame as the template. Superfolder GFP (sfGFP), a series of mutations that allow GFP to rapidly fold and mature
Green_fluorescent_protein
Realm of viruses
capsid proteins (MCPs) that contain a single vertical jelly roll fold. Singelavirians have one or two MCPs that have the single jelly roll (SJR) fold, numerous
Singelaviria
Assembly of proteins inside biological cells
change can impact the protein's ability to function or to fold correctly. Misfolded proteins have a tendency to form dense protein clumps, which are often
Protein_biosynthesis
Protein able to interconvert between multiple folds
transformer protein (TFP) also known as a metamorphic protein is a protein that can interconvert between two or more shapes (also known as folds) each having
Transformer_protein
Small protein domain found in some kinases and GTPases
The SH3-type fold is an ancient fold found in eukaryotes as well as prokaryotes. The classical SH3 domain is usually found in proteins that interact
SH3_domain
Rational design of new protein molecules
and its sequence (termed protein redesign). Rational protein design approaches make protein-sequence predictions that will fold to specific structures.
Protein_design
proteins that assist other proteins in assuming their three-dimensional fold, which is necessary for protein function. However, the fold of a protein
Evolution of molecular chaperones
Evolution_of_molecular_chaperones
American biochemist and computational biologist (born 1962)
field of protein design; they are noted for designing Top7, the first artificial protein with a novel fold. In 2017, Baker's Institute for Protein Design
David_Baker_(biochemist)
Family of proteins
perform chaperone functions by stabilizing new proteins to ensure correct folding or by helping to refold proteins that were damaged by the cell stress. This
Heat_shock_protein
Process of regulating a functional proteome
pathways within cells that control the biogenesis, folding, trafficking, and degradation of proteins present within and outside the cell. Loss of proteostasis
Proteostasis
Class of enzymes
residues within proteins as they fold. This allows proteins to quickly find the correct arrangement of disulfide bonds in their fully folded state, and therefore
Protein_disulfide-isomerase
Protein-coding gene in the species Homo sapiens
binds newly synthesized proteins as they are translocated into the ER, and maintains them in a state competent for subsequent folding and oligomerization
Binding immunoglobulin protein
Binding_immunoglobulin_protein
Diseases caused by abnormal protein structure
tissues and organs. Often the proteins fail to fold into their normal configuration; in this misfolded state, the proteins can become toxic in some way
Proteinopathy
Database of protein domains structures
automated CATH methodlogy to 188 million unique structures from the AlphaFold Protein Structure Database, identifying nearly 365 million domains, which is
CATH_database
Glycoprotein spike on a viral capsid or viral envelope
which uses its NTD to interact with a protein receptor called CEACAM1. The NTD has a galectin-like protein fold, but binds sugar molecules somewhat differently
Coronavirus_spike_protein
Protein without a fixed 3D structure
multi-domain proteins. They are sometimes considered as a separate class of proteins along with globular, fibrous and membrane proteins. IDPs are a very
Intrinsically disordered proteins
Intrinsically_disordered_proteins
Family of RNA-binding proteins
into a hierarchy of protein families, superfamilies, and folds. The LSm protein structure is an example of a small beta sheet folded into a short barrel
LSm
Enzyme
immunophilins, and parvulins. These three classes of proteins are not structurally related. Larger proteins can also contain prolyl isomerase domains
Prolyl_isomerase
Class of compounds
Chemical chaperones are a class of small molecules that function to enhance the folding and/or stability of proteins. Chemical chaperones are a broad and
Chemical_chaperone
Class of proteins
Penicillin-binding proteins (PBP) are a group of proteins that are characterized by their affinity for and binding of penicillin. They are a normal constituent
Penicillin-binding_proteins
Type of biochemical process
transcription, translation, post translational modifications, and protein folding. Proteins are made from amino acids. In humans, some amino acids can be
Protein_metabolism
Class of peptides which help cells survive freezing conditions
Antifreeze proteins (AFPs) or ice structuring proteins refer to a class of polypeptides produced by certain animals, plants, fungi and bacteria that permit
Antifreeze_protein
Protein family
expression. The AAA proteins contain two domains, an N-terminal alpha/beta domain that binds and hydrolyzes nucleotides (a Rossmann fold) and a C-terminal
AAA_proteins
Protein domain
number of repeats is 34, predicted in a protein expressed by Giardia lamblia. Ankyrin repeats typically fold together to form a single, linear solenoid
Ankyrin_repeat
Family of small proteins
UBL protein family derives its name from the first member of the class to be discovered, ubiquitin (Ub), best known for its role in regulating protein degradation
Ubiquitin-like_protein
Cell surface proteins, part of the adaptive immune system
MHC class I, MHC class II, and MHC class III. Among all those genes present in MHC, there are two types of genes coding for the proteins MHC class I molecules
Major histocompatibility complex
Major_histocompatibility_complex
Enzyme with key regulatory roles in most cells
specific cAMP-binding proteins, either transcription factors, enzymes (e.g., cAMP-dependent kinases), or ion transporters. The first class of adenylyl cyclases
Adenylyl_cyclase
Protein spanning across a biological membrane
transmembrane proteins. The amphiphilic helices remain attached to the translocon until the protein is completely synthesized and folded. If the protein remains
Transmembrane_protein
Topics referred to by the same term
Vertical trefoil and oblique trefoil, Zernike polynomials Trefoil knot fold, a protein fold This disambiguation page lists articles associated with the title
Trefoil_(disambiguation)
Proteins with backbone entangled in a knot
making up only about one percent of the proteins in the Protein Data Bank, and their folding mechanisms and function are not well understood. Although
Knotted_protein
Family of enzymes
of a protein. In addition to functioning as a purification tag, GST acts as a chaperone for the attached protein, promoting its correct folding, as well
Glutathione_S-transferase
Protein domain and superfamily
classes based on the structure of their catalytic domain (fold): class I: Rossmann-like α/β, the largest subgroup. class II: TIM β/α-barrel α/β class
AdoMet_MTase
Protein created by joining other proteins into a single polypeptide
the two entities are proteins, often linker (or "spacer") peptides are also added, which make it more likely that the proteins fold independently and behave
Fusion_protein
Protein family
A late protein is a viral protein that is formed after replication of the virus. One example is VP4 from simian virus 40 (SV40). In Human papillomavirus
Late_protein
Protein domain
TRG_NLS_MonoExtC_3 Eukaryotic Linear Motif resource motif class TRG_NLS_MonoExtN_4 Armadillo+Domain+Proteins at the U.S. National Library of Medicine Medical Subject
Armadillo_repeat
Enterotoxin produced by the bacteria Staphylococcus aureus
when it interacts with MHC class II molecules or the T-cell receptor. The N-terminal domain is also referred to as OB-fold, or in other words the oligonuclucleotide
Enterotoxin_type_B
Topics referred to by the same term
by Chris Bruno and David Howard Lee starring Evan Fong α/β barrel, a protein fold structure Izhar Cohen and the Alphabeta, musical group known for the
Alphabeta
Self-stabilizing region of a protein that binds to specific DNA sequences
A DNA-binding domain (DBD) is an independently folded protein domain that contains at least one structural motif that recognizes double- or single-stranded
DNA-binding_domain
Class of proteins
Single-stranded binding proteins (SSBs) are a class of proteins that have been identified in both viruses and organisms from bacteria to humans. Although
Single-stranded binding protein
Single-stranded_binding_protein
Class of enzymes
classification notes that 20 distinct protein folds have phosphatase activity, and 10 of these contain protein phosphatases. The CC1 fold is the most common, and includes
Protein_phosphatase
Class of copper-containing proteins
Proteins, a class of Type 1 copper proteins, are small proteins containing a cupredoxin fold. The protein structure of a Type 1 blue copper protein,
Copper_protein
Class of enzymes
The class I aaRSs feature a cytidylyltransferase-like Rossmann fold seen in proteins like glycerol-3-phosphate cytidylyltransferase, nicotinamide nucleotide
Aminoacyl_tRNA_synthetase
Realm of viruses
single-stranded DNA (ssDNA) genomes and a hallmark single jelly roll fold (SJR) major capsid protein (MCP). Viruses in the realm are commonly called microviruses
Volvereviria
Protein structural motif
solution, suggesting that hairpins could form nucleation sites for protein folding. Beta hairpins were originally categorized solely by the number of
Beta_hairpin
Arrangement of amino acid sequence
relationship between proteins whereby the proteins have a changed order of amino acids in their peptide sequence. The result is a protein structure with different
Circular permutation in proteins
Circular_permutation_in_proteins
Most expressed structure in coronaviruses
The nucleocapsid (N) protein is a protein that packages the positive-sense RNA genome of coronaviruses to form ribonucleoprotein structures enclosed within
Coronavirus nucleocapsid protein
Coronavirus_nucleocapsid_protein
Pathogenic type of misfolded protein
A prion (/ˈpriːɒn/ ) is a misfolded protein that induces folding problems in normal variants of the same protein, leading to cellular death. Prions are
Prion
Family of DNA sequences found in prokaryotic organisms
two classes. Class 1 systems use a complex of multiple Cas proteins to degrade foreign nucleic acids. Class 2 systems use a single large Cas protein for
CRISPR
Food product and protein supplement derived from Pisum sativum
Pea protein is a food product and protein supplement derived and extracted from yellow and green split peas, Pisum sativum. It can be used as a dietary
Pea_protein
Protein domain
A leucine-rich repeat (LRR) is a protein structural motif that forms an α/β horseshoe fold. It is composed of repeating 20–30 amino acid stretches that
Leucine-rich_repeat
Family of conserved regulatory molecules
role in class switch recombination. They are believed to interact with the protein activation-induced cytidine deaminase in mediating class switch recombination
14-3-3_protein
Protein domain
alpha-helix pair repeats usually fold together to produce a single, linear solenoid domain called a TPR domain. Proteins with such domains include the anaphase-promoting
Tetratricopeptide_repeat
Iron-carrying protein
universal intracellular and extracellular protein that stores iron and releases it in a controlled fashion. The protein is produced by almost all living organisms
Ferritin
Toxin protein
larger superfamily of three-finger protein domains which includes non-toxic proteins that share a similar protein fold. The group is named for its common
Three-finger_toxin
Heat shock proteins with a molecular mass around 90kDa
shock protein 90) is a chaperone protein that assists other proteins to fold properly, stabilizes proteins against heat stress, and aids in protein degradation
Hsp90
Protein family
remains unclear. The protein adopts a secondary structure consisting of five alpha helices and six antiparallel beta sheets. The fold of this family is similar
XOL-1 Switch protein N-terminal domain
XOL-1_Switch_protein_N-terminal_domain
Protein family
diameters between 24 and 42 nm and are defined by the HK97-fold of their shell protein. The HK97-fold protomer has a roughly triangular shape and consists of
Encapsulin
Protein family
protein. Later, it was demonstrated that different release factors recognize different stop codons. There are two classes of release factors. Class 1
Release_factor
Protein family
versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that
RING_finger_domain
Class of enzymes important in regulating DNA transcription
from sirtuins (class III), which fold into a Rossmann architecture and are NAD+ dependent. HDAC proteins are grouped into four classes (see above) based
Histone_deacetylase
Structural Bioinformatics
The only required input is a protein sequence for the prediction of the protein 3D structure and function. The IntFOLD output is presented via a user-friendly
IntFOLD
Accumulation of clumps of misfolded or disordered proteins
Alzheimer's, Parkinson's and prion disease. After synthesis, proteins typically fold into a particular three-dimensional conformation that is the most
Protein_aggregation
Method of protein structure prediction using other known proteins
the production of representative experimental structures for all classes of protein folds. The chief inaccuracies in homology modeling, which worsen with
Homology_modeling
Class of enzymes
phosphorylated tyrosine residues on proteins: [a protein]-tyrosine phosphate + H2O = [a protein]-tyrosine + phosphate Protein tyrosine (pTyr) phosphorylation
Protein_tyrosine_phosphatase
Class of enzymes capable of forming isopeptide bonds in certain regions of proteins
catalytic triad. Bacterial transglutaminases are single-domain proteins with a similarly-folded core. The transglutaminase found in some bacteria runs on a
Transglutaminase
Family of proteins which attach to other proteins to modify them
identical structural fold. SUMO protein has a unique N-terminal extension of 10-25 amino acids which other ubiquitin-like proteins do not have. This N-terminal
SUMO_protein
Major structure in coronaviruses
The envelope (E) protein is the smallest and least well-characterized of the four major structural proteins found in coronavirus virions. It is an integral
Coronavirus_envelope_protein
Mammalian protein found in humans
characterized by assisting protein folding and quality control, ensuring that only properly folded and assembled proteins proceed further along the secretory
Calnexin
Protein domain
developed by the Gruebele and Kelly groups into a favorite subject of protein folding studies. Among these studies, the work of Rama Ranganathan and David
WW_domain
Protein in the extracellular matrix
major constituents of the basement membrane, namely the basal lamina (the protein network foundation for most cells and organs). Laminins are vital to biological
Laminin
Protein family
c proteins can be divided in four classes based on their size, number of heme groups and reduction potentials: Small soluble cytochrome c proteins with
Cytochrome_c_family
Class of cell surface receptors coupled to G-protein-associated intracellular signaling
G protein-coupled receptors (GPCRs), also known as seven-(pass)-transmembrane domain receptors, 7TM receptors, heptahelical receptors, serpentine receptors
G_protein-coupled_receptor
Protein family
functions and can have similar structural folds, their primary sequences can be very different. Typical matrix proteins of retroviruses form an alpha helical
Retroviral_matrix_protein
Iron–sulfur proteins
their folds belonging to the α+β class. As in other bacterial ferredoxins, the [Fe4S4] unit forms a cubane-type cluster and is ligated to the protein via
Ferredoxin
British bioinformatician
Jones's main research interests are in protein structure prediction and analysis protein folding, transmembrane protein analysis, machine learning applications
David_T._Jones_(biochemist)
Large protein superfamily of cell surface and soluble proteins
The immunoglobulin superfamily (IgSF) is a large protein superfamily of cell surface and soluble proteins that are involved in the recognition, binding,
Immunoglobulin_superfamily
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PROTEIN FOLD-CLASS
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PROTEIN FOLD-CLASS
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PROTEIN FOLD-CLASS
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PROTEIN FOLD-CLASS
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