Proteins are essential macromolecules composed of long chains of amino acids linked by peptide bonds. They are crucial for the structure, function, and regulation of tissues and organs in both humans and other living organisms.

Chemical Composition and Structure:

Proteins are composed of:

Amino Acids: The building blocks of proteins, including essential and non-essential amino acids. Amino acids are linked together via peptide bonds to form polypeptide chains.

Primary Structure: The linear sequence of amino acids in the polypeptide chain.

Secondary Structure: Local structures such as alpha-helices and beta-sheets, stabilized by hydrogen bonds.

Tertiary Structure: The three-dimensional shape of the polypeptide chain, stabilized by interactions between side chains of amino acids.

Quaternary Structure (if present): The assembly of multiple polypeptide chains into a functional protein complex.

Physical Properties:

• Appearance: Varies depending on the protein and its form; can be solid, liquid, or gel-like.
• Odor: Generally odorless, but may vary based on the protein's source and treatment.
• Solubility: Depends on the protein; some are soluble in water, others in organic solvents, and some are insoluble.

Production Process:

The production of proteins can involve:

1. Extraction: Obtained from natural sources such as plants, animals, or microorganisms through extraction with solvents or mechanical methods.
2. Purification: Proteins are purified using techniques such as chromatography to separate the target proteins from impurities.
3. Modification and Formulation: Proteins may be modified or formulated for specific applications, such as improving solubility or stability.

Applications:

• Medical: Proteins are used in dietary supplements and therapeutic products to support muscle growth, tissue repair, and other bodily functions. Some therapeutic proteins are employed in treating genetic disorders and other medical conditions.
• Cosmetics: In skincare, proteins are valued for their moisturizing, strengthening, and repairing properties. They can be found in shampoos, conditioners, and treatments for skin and hair.
• Others: Proteins are also used in industrial and food applications, such as in the production of functional food ingredients and additives.

Environmental and Safety Considerations:

Proteins are generally safe and biodegradable. However, it is important to ensure they are sourced and processed sustainably. Some proteins can cause allergies or intolerances in sensitive individuals, so sensitivity testing is recommended when used in food or cosmetic products.

References__________________________________________________________________________

Pines J. Cell cycle: reaching for a role for the Cks proteins. Curr Biol. 1996 Nov 1;6(11):1399-402. doi: 10.1016/s0960-9822(96)00741-5. PMID: 8939596.

Abstract. The Cks proteins are essential components of the cyclin-dependent protein kinases that regulate mitosis in all eukaryotes, but their precise function remains obscure. The crystal structures of several Cks proteins offer insights into their roles during the cell cycle.

Paschen SA, Neupert W. Protein import into mitochondria. IUBMB Life. 2001 Sep-Nov;52(3-5):101-12. doi: 10.1080/15216540152845894. PMID: 11798021.

Abstract. Most mitochondrial proteins are encoded by the nuclear genome and thus have to be imported into mitochondria from the cytosol. Protein translocation across and into the mitochondrial membranes is a multistep process facilitated by the coordinated action of at least four specialized translocation systems in the outer and inner membranes of mitochondria. The outer membrane contains one general translocase, the TOM complex, whereas three distinct translocases are located in the inner membrane, which facilitates translocation of different classes of preproteins. The TIM23 complex mediates import of matrix-targeted preproteins with N-terminal presequences, whereas hydrophobic preproteins with internal targeting signals are inserted into the inner membrane via the TIM22 complex. The OXA translocase mediates the insertion of preproteins from the matrix space into the inner membrane. This review focuses on the structural organization and function of the import machinery of the model organisms of Saccharomyces cerevisiae and Neurospora crassa. In addition, the molecular basis of a new human mitochondrial disorder is discussed, the Mohr-Tranebjaerg syndrome. This is the first known disease, which is caused by an impaired mitochondrial protein import machinery leading to progressive neurodegeneration.

Häcker S, Krebber H. Differential export requirements for shuttling serine/arginine-type mRNA-binding proteins. J Biol Chem. 2004 Feb 13;279(7):5049-52. doi: 10.1074/jbc.C300522200. 

Abstract. Messenger RNAs are transported to the cytoplasm bound to several shuttling mRNA-binding proteins. Here, we present the characterization of Hrb1, a novel component of the transported ribonucleoprotein complex in Saccharomyces cerevisiae. The protein is similar to the other two serine/arginine (SR)-type proteins in yeast, Gbp2 and Npl3. Hrb1 is nuclear at steady state and its import is mediated by the karyopherin Mtr10. Hrb1 binds to poly(A)+ RNA in vivo and its binding is significantly increased in MTR10 mutants, suggesting a role for Mtr10 in dissociating Hrb1 from the mRNAs. Interestingly, by comparing the export requirements of all three SR proteins we find similarities but also striking differences. While the export of all three proteins is dependent on the export of mRNAs in general, as no transport is observed in mutants defective in transcription (rpb1-1) or mRNA export (mex67-5), we find specific requirements for components of the THO complex, involved in transcription elongation. While both Hrb1 and Gbp2 depend on Mft1 and Hpr1 for their nuclear export, Npl3 is exported independently of both proteins. These findings suggest that Hrb1 and Gbp2, but not Npl3, might be loaded onto the growing mRNA via the THO complex components Mtf1 and Hrp1.

Hartmann-Petersen R, Gordon C. Protein degradation: recognition of ubiquitinylated substrates. Curr Biol. 2004 Sep 21;14(18):R754-6. doi: 10.1016/j.cub.2004.09.012. PMID: 15380085.

Abstract. A cell-free system has been developed in budding yeast that provides direct evidence that the Dsk2/Dph1, Rad23/Rhp23 and Rpn10/Pus1 multi-ubiquitin-binding proteins, long implicated in substrate recognition and presentation to the 26S proteasome, actually fulfil such a role.

Ramer MD, Suman ES, Richter H, Stanger K, Spranger M, Bieberstein N, Duncker BP. Dbf4 and Cdc7 proteins promote DNA replication through interactions with distinct Mcm2-7 protein subunits. J Biol Chem. 2013 May 24;288(21):14926-35. doi: 10.1074/jbc.M112.392910. Epub 2013 Apr 2. PMID: 23549044; PMCID: PMC3663514.

Abstract. The essential cell cycle target of the Dbf4/Cdc7 kinase (DDK) is the Mcm2-7 helicase complex. Although Mcm4 has been identified as the critical DDK phosphorylation target for DNA replication, it is not well understood which of the six Mcm2-7 subunits actually mediate(s) docking of this kinase complex. We systematically examined the interaction between each Mcm2-7 subunit with Dbf4 and Cdc7 through two-hybrid and co-immunoprecipitation analyses. Strikingly different binding patterns were observed, as Dbf4 interacted most strongly with Mcm2, whereas Cdc7 displayed association with both Mcm4 and Mcm5. We identified an N-terminal Mcm2 region required for interaction with Dbf4. Cells expressing either an Mcm2 mutant lacking this docking domain (Mcm2ΔDDD) or an Mcm4 mutant lacking a previously identified DDK docking domain (Mcm4ΔDDD) displayed modest DNA replication and growth defects. In contrast, combining these two mutations resulted in synthetic lethality, suggesting that Mcm2 and Mcm4 play overlapping roles in the association of DDK with MCM rings at replication origins. Consistent with this model, growth inhibition could be induced in Mcm4ΔDDD cells through Mcm2 overexpression as a means of titrating the Dbf4-MCM ring interaction. This growth inhibition was exacerbated by exposing the cells to either hydroxyurea or methyl methanesulfonate, lending support for a DDK role in stabilizing or restarting replication forks under S phase checkpoint conditions. Finally, constitutive overexpression of each individual MCM subunit was examined, and genotoxic sensitivity was found to be specific to Mcm2 or Mcm4 overexpression, further pointing to the importance of the DDK-MCM ring interaction.

Alberts SM, Sonntag C, Schäfer A, Wolf DH. Ubx4 modulates cdc48 activity and influences degradation of misfolded proteins of the endoplasmic reticulum. J Biol Chem. 2009 Jun 12;284(24):16082-16089. doi: 10.1074/jbc.M809282200.

Abstract. Misfolded proteins of the secretory pathway are recognized in the endoplasmic reticulum (ER), retrotranslocated into the cytoplasm, and degraded by the ubiquitin-proteasome system. Right after retrotranslocation and polyubiquitination, they are extracted from the cytosolic side of the ER membrane through a complex consisting of the AAA ATPase Cdc48 (p97 in mammals), Ufd1, and Npl4. This complex delivers misfolded proteins to the proteasome for final degradation. Extraction, delivery, and processing of ERAD (ER-associated degradation) substrates to the proteasome requires additional cofactors of Cdc48. Here we characterize the UBX domain containing protein Ubx4 (Cui1) as a crucial factor for the degradation of polyubiquitinated proteins via ERAD. Ubx4 modulates the Cdc48-Ufd1-Npl4 complex to guarantee its correct function. Mutant variants of Ubx4 lead to defective degradation of misfolded proteins and accumulation of polyubiquitinated proteins bound to Cdc48. We show the requirement of the UBX domain of Ubx4 for its function in ERAD. The observation that Ubx2 and Ubx4 are not found together in one complex with Cdc48 suggests several distinct steps in modulating the activity and localization of Cdc48 in ERAD.