Higher-order structures of proteins

Factors that promote the folding of proteins include covalent -S-S- disulfide links between cysteine residues (14), Coulombic interactions between ions (which depend on the degree of protonation of groups and therefore on the pH), hydrogen bonding (such as O-H—O), van der Waals interactions, and hydrophobic interactions. The clustering of nonpolar, hydrophobic amino acids into the interior of a protein is driven primarily by hydrophobic interactions (Section 2.7). 

Proteins can also seh-assemble into rather large aggregates. Collagen (Atlas P4), the most abundant protein in mammals and responsible for imparting mechanical strength to tissues and organs, consists of three long hehces wound around each other. The protein actin forms thin, rodlike filaments that, when associated with several copies of the protein myosin, play an important role in the mechanism of muscle contraction. The microtubules that participate in the 

Data from T.E. Creighton, Proteins structures and molecular properties  

Not all protein aggregates are beneficial. In patients afflicted with sickle-cell anemia, hemoglobin molecules aggregate into rods, rendering the red blood cell unable to transport O2 efficiently. Also, the presence of aggregates of proteins in the brain appears to be associated with severed serious conditions. For example, the amyloid plaques found in postmortem analysis of the brains of patients with Alzheimer s disease are a mixture of damaged neurons and aggregates of the fi amyloid protein, which is an extended antiparallel p sheet. 

Of crucial biological importance are the conformations adopted by nuoleio acids, the key components of the mechanism of storage and transfer of genetio information in biological cells. 

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Ion Mobility Measurements for Studying Higher-Order Structures of Proteins 488... 

How about the higher order structure of proteins We have said that secondary structure is determined by simply folding the primary chain so as to achieve the largest number of H bonds between different parts of the chain. However, in the proteins toother much more powerful bond is provided by the amino acid fysteine ... 

The Role of Hydrogen Exchange Mass Spectrometry in Assessing the Consistency and Comparability of the Higher-Order Structure of Protein Biopharmaceuticals... 

Wei, H., Mo, J., Tao, L., et al. (2014) Hydrogen/Deuterium Exchange Mass Spectrometry for Probing Higher Order Structure of Protein Therapeutics Methodology and Applications. Drug Discovery Today, 19(1), 95-102. 

Of the proteins (amino acids), cysteine has thiol (SH) on the side chain and thus it forms disulfide bonds intramolecularly or intermolecularly and contributes to the formation and stabilization of the higher-order structures of proteins. Because the formation of a disulfide bond by thiols is a... 

Figure 3 Examples of higher-order structure in proteins the a-helix and P-sheet.

The essential distinction between the approaches used to formulate and evaluate proteins, compared with conventional low molecular weight drugs, lies in the need to maintain several levels of protein structure and the unique chemical and physical properties that these higher-order structures convey. Proteins are condensation polymers of amino acids, joined by peptide bonds. The levels of protein architecture are typically described in terms of the four orders of structure [23,24] depicted in Fig. 2. The primary structure refers to the sequence of amino acids and the location of any disulfide bonds. Secondary structure is derived from the steric relations of amino acid residues that are close to one another. The alpha-helix and beta-pleated sheet are examples of periodic secondary structure. Tertiary... 

Of the five snRNAs, U2 and U6 interact with the reaction site (the 5 splice site and the branch point) in the first chemical step. These two snRNAs are known to anneal together to form a stable-based paired structure in the absence of proteins and in the presence of ions as shown in Fig. 13, with U2 acting as an inducer molecule that displaces the U4 (that is an antisense molecule that regulates the catalytic function of U6 RNA) from the initially formed U4-U6 duplex. The secondary (or higher ordered) structure of the U2-U6 complex consists of the active site of the spliceosome. Recent data suggests that these two snRNAs function as the catalytic domain of the spliceosome that catalyzes the first step of the splicing reaction [145]. 

In the chromatin of eukaryotic cells DNA forms a coiled-coil structure with an approximately equal weight of a mixture of five basic proteins known as histones. Four of these histones in pairs form an octa-mer around which the DNA duplex occurs in a left-handed helix. The DNA octamer complex is called a nucleosome. Each nucleosome contains about 140 base pairs of DNA in a nuclease-resistant nucleosome core and approximately 60 base pairs of spacer between core particles. Histone HI binds to the chromatin independently of the octamer and is the first histone to dissociate from the chromatin when the ionic strength is raised. Beyond the nucleosome the higher order structure of the chromosome involves coiled-coil structures with varying degrees of regularity. 

Heterochromatin protein 1, binds to heterochromatin and interacts with numerous partner proteins to organize the higher-order structure of heterochromatin... 

The CP/MAS NMR spectra of tropomyosin in the solid state were measured, in order to elucidate the higher order structure of the protein through the observation of the NMR chemical shifts of the amino acid residues, and their mobility [100-102]. A CP/MAS NMR spectrum of... 

SEC. Another liquid chromatographic technique applied in biopharmaceutical characterization is SEC. In this technique, compounds are separated based on size and shape. In contrast to RP-HPLC, SEC has a low resolving power that has limited the application of the technique. The main application of SEC in pharmaceutical analysis is the determination of the native size of a protein and the quantihcation of protein aggregates. Typically protein-friendly conditions are employed in SEC that are expected not to affect the higher order structure of the protein. 

Severai detaiied reviews on the stabiiity of proteins and protein pharmaceuticais written for pharmaceutical scientisls are available (43,45,46,47,48,49,50). A brief overview of these resources foiiows and provides additionai information. The instability of proteins, including protein pharmaceuticals, can be separated into two distinct ciasses. Chemicai instabiiity resuits from bond formation or cleavage yielding a modification of the protein and a new chemical entity. Physical instability involves a change to the secondary or higher-order structure of the protein rather than a covalent bond-breaking modification. 

Most of the interest in the hydrogen-bond-transmitted spin-spin coupling constants lies in their potential application for determination of the higher order structures of biomolecules proteins and nucleic acids. Consequently, the theoretical papers reporting calculations of the hydrogen-bond-transmitted spin-spin coupling constants in models of biological systems are abundant. 

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