Page last updated: 2024-10-24

protein polymerization

Definition

Target type: biologicalprocess

The process of creating protein polymers, compounds composed of a large number of component monomers; polymeric proteins may be made up of different or identical monomers. Polymerization occurs by the addition of extra monomers to an existing poly- or oligomeric protein. [GOC:ai]

Protein polymerization is a fundamental biological process responsible for assembling long chains of proteins, known as polymers. This process is crucial for creating complex cellular structures and performing various cellular functions. Here's a detailed breakdown of protein polymerization:

**1. Monomers: The Building Blocks**

Protein polymerization begins with individual amino acids, the basic units of proteins. Each amino acid consists of:

* **Amino group (NH2):** This group provides the building block for the peptide bond.
* **Carboxyl group (COOH):** This group participates in peptide bond formation.
* **Side chain (R group):** This unique group distinguishes one amino acid from another, influencing the protein's overall structure and function.

**2. Peptide Bond Formation**

The polymerization process involves the formation of peptide bonds between adjacent amino acids. This process occurs through a dehydration reaction, where a water molecule is removed:

* **Dehydration reaction:** The carboxyl group of one amino acid reacts with the amino group of another amino acid, releasing a water molecule. This forms a covalent bond called a peptide bond.

**3. Polypeptide Chain Formation**

As peptide bonds form between amino acids, a chain of linked amino acids called a polypeptide chain emerges. The polypeptide chain grows one amino acid at a time, with a specific sequence determined by the genetic code.

**4. Protein Folding**

The polypeptide chain doesn't remain as a simple linear structure. It folds into a unique three-dimensional shape, guided by interactions between the amino acid side chains. These interactions include:

* **Hydrogen bonds:** Weak bonds formed between hydrogen atoms and electronegative atoms (oxygen or nitrogen).
* **Ionic bonds:** Electrostatic interactions between oppositely charged side chains.
* **Van der Waals forces:** Weak, short-range attractions between nonpolar molecules.
* **Disulfide bonds:** Covalent bonds formed between cysteine residues, contributing to protein stability.

**5. Protein Structure**

The folded polypeptide chain forms the protein's final structure, which can be classified into four levels of organization:

* **Primary structure:** The linear sequence of amino acids in the polypeptide chain.
* **Secondary structure:** Local folding patterns within the polypeptide chain, such as alpha-helices and beta-sheets.
* **Tertiary structure:** The overall three-dimensional shape of a single polypeptide chain.
* **Quaternary structure:** The arrangement of multiple polypeptide chains, forming a multimeric protein complex.

**6. Importance of Protein Polymerization**

Protein polymerization is essential for:

* **Building structural components:** Proteins provide structural support to cells and tissues, such as collagen in connective tissues.
* **Enzymatic activity:** Enzymes are proteins that catalyze biochemical reactions within cells.
* **Hormonal signaling:** Some hormones are proteins that regulate physiological processes.
* **Transport and storage:** Proteins can transport molecules across cell membranes or store nutrients.
* **Immune defense:** Antibodies, which are proteins, protect the body from foreign invaders.

**In summary, protein polymerization is a complex and highly regulated process that assembles amino acids into functional proteins. This process is crucial for life, enabling cells to perform diverse and essential functions.'
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Proteins (6)

ProteinDefinitionTaxonomy
Cell division protein FtsZA cell division protein FtsZ that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0A9A6]Escherichia coli K-12
Cell division protein FtsZA cell division protein FtsZ that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0A9A6]Escherichia coli K-12
Prothrombin A prothrombin that is encoded in the genome of cow. [OMA:P00735, PRO:DNx]Bos taurus (cattle)
Dynamin-2A dynamin-2 that is encoded in the genome of human. [PRO:DNx, UniProtKB:P50570]Homo sapiens (human)
Phospholipid hydroperoxide glutathione peroxidaseA phospholipid hydroperoxide glutathione peroxidase GPX4 that is encoded in the genome of human. [PRO:DNx, UniProtKB:P36969]Homo sapiens (human)
Microtubule-associated protein tauA microtubule-associated protein tau that is encoded in the genome of human. [PRO:DAN]Homo sapiens (human)

Compounds (49)

CompoundDefinitionClassesRoles
benzamidinebenzamidine : A carboxamidine that is benzene carrying an amidino group.

benzamidine: RN given refers to parent cpd
benzenes;
carboxamidine
serine protease inhibitor
bis(5-amidino-2-benzimidazolyl)methanebis(5-amidino-2-benzimidazolyl)methane: aromatic diamidine which has a significant suppressive effect on the cytopathology & yield of respiratory synctial (RS) virus; RN given refers to parent cpd
dapiDAPI: RN given refers to parent cpd.indolesfluorochrome
gentian violetcrystal violet cation : An iminium ion that is malachite green cation in which the hydrogen at the para- psition of the monosubstituted phenyl group is replaced by a dimethylamino group.iminium ionantibacterial agent;
antifungal agent
lansoprazoleLansoprazole: A 2,2,2-trifluoroethoxypyridyl derivative of timoprazole that is used in the therapy of STOMACH ULCERS and ZOLLINGER-ELLISON SYNDROME. The drug inhibits H(+)-K(+)-EXCHANGING ATPASE which is found in GASTRIC PARIETAL CELLS. Lansoprazole is a racemic mixture of (R)- and (S)-isomers.benzimidazoles;
pyridines;
sulfoxide
anti-ulcer drug;
EC 3.6.3.10 (H(+)/K(+)-exchanging ATPase) inhibitor
3,7-bis(dimethylamino)phenothiazin-5-ium3,7-bis(dimethylamino)phenothiazin-5-ium : An organic cation that is phenothiazin-5-ium substituted by dimethylamino groups at positions 3 and 7. The chloride salt is the histological dye 'methylene blue'.organic cation
nevirapinenevirapine : A dipyridodiazepine that is 5,11-dihydro-6H-dipyrido[3,2-b:2',3'-e][1,4]diazepine which is substituted by methyl, oxo, and cyclopropyl groups at positions 4, 6, and 11, respectively. A non-nucleoside reverse transcriptase inhibitor with activity against HIV-1, it is used in combination with other antiretrovirals for the treatment of HIV infection.

Nevirapine: A potent, non-nucleoside reverse transcriptase inhibitor used in combination with nucleoside analogues for treatment of HIV INFECTIONS and AIDS.
cyclopropanes;
dipyridodiazepine
antiviral drug;
HIV-1 reverse transcriptase inhibitor
aurinaurin: structurediarylmethane
methylene bluemethylene blue : An organic chloride salt having 3,7-bis(dimethylamino)phenothiazin-5-ium as the counterion. A commonly used dye that also exhibits antioxidant, antimalarial, antidepressant and cardioprotective properties.

Methylene Blue: A compound consisting of dark green crystals or crystalline powder, having a bronze-like luster. Solutions in water or alcohol have a deep blue color. Methylene blue is used as a bacteriologic stain and as an indicator. It inhibits GUANYLATE CYCLASE, and has been used to treat cyanide poisoning and to lower levels of METHEMOGLOBIN.
organic chloride saltacid-base indicator;
antidepressant;
antimalarial;
antimicrobial agent;
antioxidant;
cardioprotective agent;
EC 1.4.3.4 (monoamine oxidase) inhibitor;
EC 3.1.1.8 (cholinesterase) inhibitor;
EC 4.6.1.2 (guanylate cyclase) inhibitor;
fluorochrome;
histological dye;
neuroprotective agent;
physical tracer
tolonium chloridetolonium chloride : An organic chloride salt having 3-amino-7-(dimethylamino)-2-methylphenothiazin-5-ium (tolonium) as the counterion. It is a blue nuclear counterstain that can be used to demonstrate Nissl substance and is also useful for staining mast cell granules, both in metachromatic and orthochromatic techniques.

Tolonium Chloride: A phenothiazine that has been used as a hemostatic, a biological stain, and a dye for wool and silk. Tolonium chloride has also been used as a diagnostic aid for oral and gastric neoplasms and in the identification of the parathyroid gland in thyroid surgery.
Berberine chloride (TN)organic molecular entity
azure aazure A : An organic chloride salt having 3-amino-7-(dimethylamino)phenothiazin-5-ium as the counterion. It is used in making azure eosin stains for blood smear staining.

Azure A: RN given refers to chloride
1,2-di(5-amidino-2-benzofuranyl)ethane1,2-di(5-amidino-2-benzofuranyl)ethane: preferential inhibitor of bovine factor Xa; structure given in first source
efavirenzefavirenz : 1,4-Dihydro-2H-3,1-benzoxazin-2-one substituted at the 4 position by cyclopropylethynyl and trifluoromethyl groups (S configuration) and at the 6 position by chlorine. A non-nucleoside reverse transcriptase inhibitor with activity against HIV, it is used with other antiretrovirals for combination therapy of HIV infection.

efavirenz: HIV-1 reverse transcriptase inhibitor
acetylenic compound;
benzoxazine;
cyclopropanes;
organochlorine compound;
organofluorine compound
antiviral drug;
HIV-1 reverse transcriptase inhibitor
thioninethionine : An organic chloride salt composed of 3,7-diaminophenothiazin-5-ium and chloride ions in a 1:1 ratio. A strongly metachromatic dye, useful for the staining of acid mucopolysaccharides. It is also a common nuclear stain and can be used for the demonstration of Nissl substance in nerve cells of the CNS.

thionine: do not confuse with the thionins which is a class of polypeptides; RN above is for the chloride;
epigallocatechin gallate(-)-epigallocatechin 3-gallate : A gallate ester obtained by the formal condensation of gallic acid with the (3R)-hydroxy group of (-)-epigallocatechin.

epigallocatechin gallate: a steroid 5alpha-reductase inhibitor and antimutagen in green tea (Camellia sinensis)
flavans;
gallate ester;
polyphenol
antineoplastic agent;
antioxidant;
apoptosis inducer;
geroprotector;
Hsp90 inhibitor;
neuroprotective agent;
plant metabolite
1,2,3,4,6-pentakis-O-galloyl-beta-D-glucose1,2,3,4,6-pentakis-O-galloyl-beta-D-glucose : A galloyl-beta-D-glucose compound having five galloyl groups in the 1-, 2-, 3-, 4- and 6-positions.

pentagalloylglucose: pentahydroxy gallic acid ester of glucose; a phytogenic antineoplastic agent and antibacterial agent
gallate ester;
galloyl beta-D-glucose
anti-inflammatory agent;
antineoplastic agent;
geroprotector;
hepatoprotective agent;
plant metabolite;
radiation protective agent;
radical scavenger
azure bazure B : An organic chloride salt having 3-(dimethylamino)-7-(methylamino)phenothiazin-5-ium as the counterion. It is used in making azure eosin stains for blood smear staining and is an active metabolite of methylene blue.

Azure B: RN given refers to chloride
epicatechin(-)-epicatechin : A catechin with (2R,3R)-configuration.catechin;
polyphenol
antioxidant
leupeptinaldehyde;
tripeptide
bacterial metabolite;
calpain inhibitor;
cathepsin B inhibitor;
EC 3.4.21.4 (trypsin) inhibitor;
serine protease inhibitor
mci 9038peptide
dx 9065
efegatranefegatran: RN & structure given in first source; RN given refers to parent cpd (D)-isomer
5-amidinoindole
n(alpha)-(4-toluenesulfonyl)-4-amidinophenylalanylpiperidineN(alpha)-(4-toluenesulfonyl)-4-amidinophenylalanylpiperidine: binds to thrombin & trypsin; structure given in first source
1,2-bis(5-amidino-2-benzimidazolyl)ethane1,2-bis(5-amidino-2-benzimidazolyl)ethane: RN given refers to parent cpd
2-(4-amidinophenyl)-1-benzofuran-5-carboxamidine2-(4-amidinophenyl)-1-benzofuran-5-carboxamidine: structure given in first source
4-guanidinobenzoate4-guanidinobenzoate: RN given refers to parent cpd

4-guanidinobenzoic acid : Benzoic acid substituted at the para position by a guanidino group.
benzoic acids;
guanidines
dichamanetindichamanetin: structure in first sourcediarylheptanoidmetabolite
Pedunculaginpedunculagin: from the walnut (Juglans regia) pellicletannin
cinnamaldehyde(E)-cinnamaldehyde : The E (trans) stereoisomer of cinnamaldehyde, the parent of the class of cinnamaldehydes.

3-phenylprop-2-enal : A member of the class of cinnamaldehydes that is prop-2-enal in which a hydrogen at position 3 has been replaced by a phenyl group. The configuration of the double bond is not specified; the name "cinnamaldehyde" is widely used to refer to the E (trans) isomer.
3-phenylprop-2-enal;
cinnamaldehydes
antifungal agent;
EC 4.3.1.24 (phenylalanine ammonia-lyase) inhibitor;
flavouring agent;
hypoglycemic agent;
plant metabolite;
sensitiser;
vasodilator agent
curcumincurcumin : A beta-diketone that is methane in which two of the hydrogens are substituted by feruloyl groups. A natural dyestuff found in the root of Curcuma longa.

Curcumin: A yellow-orange dye obtained from tumeric, the powdered root of CURCUMA longa. It is used in the preparation of curcuma paper and the detection of boron. Curcumin appears to possess a spectrum of pharmacological properties, due primarily to its inhibitory effects on metabolic enzymes.
aromatic ether;
beta-diketone;
diarylheptanoid;
enone;
polyphenol
anti-inflammatory agent;
antifungal agent;
antineoplastic agent;
biological pigment;
contraceptive drug;
dye;
EC 1.1.1.205 (IMP dehydrogenase) inhibitor;
EC 1.1.1.21 (aldehyde reductase) inhibitor;
EC 1.1.1.25 (shikimate dehydrogenase) inhibitor;
EC 1.6.5.2 [NAD(P)H dehydrogenase (quinone)] inhibitor;
EC 1.8.1.9 (thioredoxin reductase) inhibitor;
EC 2.7.10.2 (non-specific protein-tyrosine kinase) inhibitor;
EC 3.5.1.98 (histone deacetylase) inhibitor;
flavouring agent;
food colouring;
geroprotector;
hepatoprotective agent;
immunomodulator;
iron chelator;
ligand;
lipoxygenase inhibitor;
metabolite;
neuroprotective agent;
nutraceutical;
radical scavenger
2-chloro-N-heptyl-N-(3-methylphenyl)acetamideanilide
N-(1,3-benzodioxol-5-yl)-2-chloro-N-[(2-prop-2-enoxyphenyl)methyl]acetamidebenzodioxoles
ML162ML162 : A monochlorobenzene that is benzene substituted by (chloroacetyl){2-oxo-2-[(2-phenylethyl)amino]-1-(thiophen-2-yl)ethyl}amino, chloro and methoxy groups at positions 1, 3 and 4, respectively. It is a covalent inhibitor of glutathione peroxidase 4 (GPX4) that induces ferroptosis in cells.monochlorobenzenes;
monomethoxybenzene;
organochlorine compound;
secondary carboxamide;
tertiary carboxamide;
thiophenes
EC 1.11.1.9 (glutathione peroxidase) inhibitor;
ferroptosis inducer
quercetin7-hydroxyflavonol;
pentahydroxyflavone
antibacterial agent;
antineoplastic agent;
antioxidant;
Aurora kinase inhibitor;
chelator;
EC 1.10.99.2 [ribosyldihydronicotinamide dehydrogenase (quinone)] inhibitor;
geroprotector;
phytoestrogen;
plant metabolite;
protein kinase inhibitor;
radical scavenger
gossypetingossypetin : A hexahydroxyflavone having the hydroxy groups placed at the 3-, 3'-, 4'-, 5- 7- and 8-positions.

gossypetin: inhibits activity of penicillinase enzyme in E coli
7-hydroxyflavonol;
hexahydroxyflavone
plant metabolite
myricetin7-hydroxyflavonol;
hexahydroxyflavone
antineoplastic agent;
antioxidant;
cyclooxygenase 1 inhibitor;
food component;
geroprotector;
hypoglycemic agent;
plant metabolite
rutinquercetin-3-O-rutinoside: structure in first sourceflavonoids;
glycoside
su 4312SU4312 : A member of the class of oxindoles that is 3-methyleneoxindole in which one of the hydrogens of the methylene group has been replaced by a p-(dimethylamino)phenyl group. SU 4312 is a vascular endothelial growth factor (VEGF) receptor protein tyrosine kinase 1/2 and platelet derived growth factor (PDGF) receptor inhibitor. It also inhibits the neuronal nitric oxide synthase (NOS) and exhibits neuroprotection against NO-mediated neurotoxicity.
n-alpha-(2,4,6-triisopropyl-phenylsulfonyl)-3-amidino-(l)-phenyl-alanine-4-ethoxycarbonyl-piperazide hydrochloride
lb 30057
2-(4'-(methylamino)phenyl)-6-hydroxybenzothiazole
dynole 34-2dynole 34-2: a dynamin inhibitor; structure in first source
no. 407No. 407: RN in Chemline for preparation 407: 60267-56-3; structure in first source
chrysophaentin achrysophaentin A: structure in first source
ML-210ML-210 : An N-acylpiperazine that is piperazine substituted by 5-methyl-4-nitro-1,2-oxazole-3-carbonyl and bis(4-chlorophenyl)methyl groups at positions 1 and 4, respectively. It is a glutathione peroxidase 4 (GPX4) inhibitor which induces ferroptosis in cancer cells expressing the RAS oncogene.C-nitro compound;
diarylmethane;
isoxazoles;
monochlorobenzenes;
N-acylpiperazine;
N-alkylpiperazine;
tertiary carboxamide
antineoplastic agent;
EC 1.11.1.9 (glutathione peroxidase) inhibitor;
ferroptosis inducer;
prodrug
cnb 001
hydrazinocurcuminhydrazinocurcumin : A pyrazole obtained by cyclocodensation of the two carbonyl groups of curcumin with hydrazine.

hydrazinocurcumin: structure in first source
aromatic ether;
olefinic compound;
polyphenol;
pyrazoles
angiogenesis modulating agent;
antineoplastic agent;
EC 2.3.1.48 (histone acetyltransferase) inhibitor;
EC 2.7.11.1 (non-specific serine/threonine protein kinase) inhibitor