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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Protein | Definition | Taxonomy |
---|---|---|
Cell division protein FtsZ | A 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 FtsZ | A 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-2 | A dynamin-2 that is encoded in the genome of human. [PRO:DNx, UniProtKB:P50570] | Homo sapiens (human) |
Phospholipid hydroperoxide glutathione peroxidase | A phospholipid hydroperoxide glutathione peroxidase GPX4 that is encoded in the genome of human. [PRO:DNx, UniProtKB:P36969] | Homo sapiens (human) |
Microtubule-associated protein tau | A microtubule-associated protein tau that is encoded in the genome of human. [PRO:DAN] | Homo sapiens (human) |
Compound | Definition | Classes | Roles |
---|---|---|---|
benzamidine | benzamidine : 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)methane | bis(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 | ||
dapi | DAPI: RN given refers to parent cpd. | indoles | fluorochrome |
gentian violet | crystal 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 ion | antibacterial agent; antifungal agent |
lansoprazole | Lansoprazole: 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-ium | 3,7-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 | |
nevirapine | nevirapine : 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 |
aurin | aurin: structure | diarylmethane | |
methylene blue | methylene 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 salt | acid-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 chloride | tolonium 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 a | azure 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)ethane | 1,2-di(5-amidino-2-benzofuranyl)ethane: preferential inhibitor of bovine factor Xa; structure given in first source | ||
efavirenz | efavirenz : 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 |
thionine | thionine : 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-glucose | 1,2,3,4,6-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 b | azure 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 |
leupeptin | aldehyde; tripeptide | bacterial metabolite; calpain inhibitor; cathepsin B inhibitor; EC 3.4.21.4 (trypsin) inhibitor; serine protease inhibitor | |
mci 9038 | peptide | ||
dx 9065 | |||
efegatran | efegatran: RN & structure given in first source; RN given refers to parent cpd (D)-isomer | ||
5-amidinoindole | |||
n(alpha)-(4-toluenesulfonyl)-4-amidinophenylalanylpiperidine | N(alpha)-(4-toluenesulfonyl)-4-amidinophenylalanylpiperidine: binds to thrombin & trypsin; structure given in first source | ||
1,2-bis(5-amidino-2-benzimidazolyl)ethane | 1,2-bis(5-amidino-2-benzimidazolyl)ethane: RN given refers to parent cpd | ||
2-(4-amidinophenyl)-1-benzofuran-5-carboxamidine | 2-(4-amidinophenyl)-1-benzofuran-5-carboxamidine: structure given in first source | ||
4-guanidinobenzoate | 4-guanidinobenzoate: RN given refers to parent cpd 4-guanidinobenzoic acid : Benzoic acid substituted at the para position by a guanidino group. | benzoic acids; guanidines | |
dichamanetin | dichamanetin: structure in first source | diarylheptanoid | metabolite |
Pedunculagin | pedunculagin: from the walnut (Juglans regia) pellicle | tannin | |
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 |
curcumin | curcumin : 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)acetamide | anilide | ||
N-(1,3-benzodioxol-5-yl)-2-chloro-N-[(2-prop-2-enoxyphenyl)methyl]acetamide | benzodioxoles | ||
ML162 | ML162 : 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 |
quercetin | 7-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 | |
gossypetin | gossypetin : 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 |
myricetin | 7-hydroxyflavonol; hexahydroxyflavone | antineoplastic agent; antioxidant; cyclooxygenase 1 inhibitor; food component; geroprotector; hypoglycemic agent; plant metabolite | |
rutin | quercetin-3-O-rutinoside: structure in first source | flavonoids; glycoside | |
su 4312 | SU4312 : 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 34-2 | dynole 34-2: a dynamin inhibitor; structure in first source | ||
no. 407 | No. 407: RN in Chemline for preparation 407: 60267-56-3; structure in first source | ||
chrysophaentin a | chrysophaentin A: structure in first source | ||
ML-210 | ML-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 | |||
hydrazinocurcumin | hydrazinocurcumin : 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 |