PROTEINS AND PEPTIDES HIGHER-ORDER STRUCTURES

Fundamentals of Contemporary Mass Spectrometry, by Chhabil Dass Copyright 2007 John Wiley Sons, Inc. 

With the development of relatively softer ionization techniques (ESI and MALDI), mass spectrometry has emerged as an option for the determination of conformational changes in proteins [2,16-23], It is believed that the solution-phase structure of a protein is largely preserved during ionization by these two methods. Therefore, the ESI and MALDI mass spectra of a protein reflect the features of its aqueous solution chemistry. The multiple-charging feature of ESI is also a valuable asset because it allows the study of much larger proteins. In this chapter a broad outline of the commonly used mass spectrometry-based techniques is presented. 

Mass spectrometry offers several distinct advantages, snch as sensitivity, protein stability, and extended molecular mass, and also provides information complementary to NMR. The solubihty and pnrity of a protein arc of less concern. Furthermore, exchange rates of the most rapidly exchanging amide hydrogens can be determined. Therefore, mass spectrometry can reveal stmctnral details on transient or folding intermediates. These species may not be accessible by other conventional techniques mentioned above (e.g., NMR, CD, llnorescence) because they provide information that represents an average of entire protein ensembles. The NMR approach, on the other hand, is snperior with respect to resolution also the precious protein sample is not destroyed. 

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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... 

Ramachandran s stereochemical plot diagram) of dipeptides has been widely used to predict the secondary structures of proteins [306-309]. It is well known that the calculations on the polypeptides are limited by the number of atoms and hence high level ab initio and DFT calculations have been possible recently only. Several theoretical calculations with different levels of accuracy have been made on the polypeptides to study the < )- 1> plot distribution, H-bonding interactions, and stability [1-4, 308-322]. In the stability of polypeptides and proteins, H-bond plays an important role in the formation of the secondary structures such as the a-helix, (3-sheet, etc., and higher-order structures [1-4]. Quantum chemical calculations on some of the secondary structures in peptides and proteins ((3-sheets, (3-turns, and y-turns) at the HF and MP2 levels have been performed with special emphasis to the H-bonded structures... 

Peptide and protein stability is highly dependent on amino acid composition and sequence and, for proteins, on the formation of higher-order structures, which means that every protein has to be considered as a special case. Given a certain sequence, external factors such as pH, ionic strength, temperature, pressure, and the existence of interfaces can also have a tremendous impact on peptide and protein integrity [24], There are two main degradation pathways ... 

The term stability can have different meanings in the context of protein formulations. A stable pharmaceutical product according to the U.S. Food and Drug Administration definition is one that deteriorates no more than 10% in 2 years [25], Conformational and physical stability of a protein are defined as the ability of the protein to retain its tertiary structure [6], Noncovalent degradation is relevant mainly for proteins having higher order structures, rather than peptides. Native structure is maintained by a balance of noncovalent interactions such as hydrogen bonds, 2005 by CRC Press LLC... 

The wealth of natural examples provides immense inspiration for the molecular design of novel peptide-based materials that can be potentially applied as devices, sensors, and biomaterials for medical applications. In addition to hierarchical self-assembly, nature uses other mechanisms, for example, enzyme-mediated covalent cross-linking, to build up structural proteins and higher-ordered structures. In the following sections we will focus on manmade peptide-based materials that belong to the three classes listed below. They will be split with respect to the underlying design concept into materials formed by ... 

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