The secondary structure of proteins

Plenary 2. S A Asher et al, e-mail address asher ,vms.cis.pitt.edu/asher+ (RRS, TRRRS). UV RRS is used to probe methodically the secondary structure of proteins and to follow unfolding dynamics. Developing a library based approach to generalize the mediod to any protein. 

The cylinder model is used to characterize the helices in the secondary structure of proteins (see the helices in Figure 2-124c),... 

Chou P Y and G D Fasman 1978. Prediction of the Secondary Structure of Proteins from Tlieir Amino Acid Sequence. Advances in Enzymology 47 45-148. 

PY Chou, CD Easman. Prediction of the secondary structure of proteins from their ammo acid sequence. Adv Enzymol Relat Areas Mol Biol 47 45-148, 1978. 

Propiolactone is one example. It will alkylate amino, imino, hydroxyl and carboxyl groups, all of which occur in proteins, and react also with thiol and disulphide groups responsible for the secondary structure of proteins and the activity of some enzymes. 

In proteins in particular the peptide bonds contribute to the CD-spectra of the macromolecule. Here, CD-spectra reflect the secondary structure of proteins, which are derived from CD-spectra of model macromolecules with only one defined secondary structure (like poly-L-lysine at given pH values) or based on spectra of proteins with known structures (e.g.,from X-ray crystallography). The amount of a-helices or -sheets in the unknown structure is calculated by linear combination of the reference spectra [150,151]. 

Figure 11.2 The secondary structure of proteins. The simplest spatial arrangement of amino acids in a polypeptide chain is as a fully extended chain (a) which has a regular backbone structure due to the bond angles involved and from which the additional atoms, H and O, and the amino acid residues, R, project at varying angles. The helical form (b) is stabilized by hydrogen bonds between the —NH group of one peptide bond and the —CO group of another peptide bond. The amino acid residues project from the helix rather than internally into the helix.

Noncovalent interactions play a key role in biodisciplines. A celebrated example is the secondary structure of proteins. The 20 natural amino acids are each characterized by different structures with more or less acidic or basic, hydrophilic or hydrophobic functionalities and thus capable of different intermolecular interactions. Due to the formation of hydrogen bonds between nearby C=0 and N-H groups, protein polypeptide backbones can be twisted into a-helixes, even in the gas phase in the absence of any solvent." A protein function is determined more directly by its three-dimensional structure and dynamics than by its sequence of amino acids. Three-dimensional structures are strongly influenced by weak non-covalent interactions between side functionalities, but the central importance of these weak interactions is by no means limited to structural effects. Life relies on biological specificity, which arises from the fact that individual biomolecules communicate through non-covalent interactions." " Molecular and chiral recognition rely on... 

Fourier transform infrared/photoacoustic spectroscopy (FT-IR/PAS) can be used to evaluate the secondary structure of proteins, as demonstrated by experiments on concanavalin A, hemoglobin, lysozyme, and trypsin, four proteins having different distributions of secondary... 

In amides, the lone electron pair on the nitrogen atom promotes resonance stabilization of the carbonyl region (see Figure 9-14). This stabilization is important not only to amides, but also to the secondary structure of proteins. 

Heat, strong acids or bases, ethanol, or heavy-metal ions irreversibly alter the secondary structure of proteins (see below). This process, known as denaturation, is exemplified by the heat-induced coagulation and hardening of egg white (albumin). Denaturation destroys the physiological activity of proteins. 

Fig. 18.2. Raman spectroscopy of live, fixed and dried cells. Raman spectrum of a single cell construct provides a unique biochemical fingerprint , which provides a snap shot of the entire biomolecular components. The mean Raman spectra (4 separate measurements) of a single live, fixed and desiccated epithelial cell are compared (a). Fixation and desiccation influence cellular biochemistry. Desiccation distorts Raman bands describing all cellular biopolymers, especially proteins. Distinct biochemical changes in the secondary structure of proteins in the fixed cell can also be detected. Similar results were obtained in several other cells when analysed under similar conditions. Light microscope pictures of the cells in live cell culture (b), and after fixation (c) and desiccation (d) are shown. Scalebar = 10 pm. [3]...

The secondary amide group, -C(0)NHR, is ubiquitous in protein structures where hydrogen bonding from the amide NH group to the carbonyl oxygen atom is responsible for much of the secondary structure of proteins such as a-helices and (I-sheets. The electron withdrawing effect of the carbonyl oxygen... 

Secondary protein structures are the local regular and random conformations assumed by sections of the peptide chains found in the structures of peptides and proteins. The main regular conformations found in the secondary structures of proteins are the a-helix, the fl-pleated sheet and the triple helix (Figure 1.8). These and other random conformations are believed to be mainly due to intramolecular hydrogen bonding between different sections of the peptide chain. 

CD spectroscopy is not limited to the study of small molecules, and has become extremely important in the characterization of biomolecules. The secondary structure of proteins can be characterized through studies of the CD associated with the amide chromophores. Using a combination of models and calibration spectra, it is possible to deduce the relative contributions to the overall secondary structure made by a-helix, antiparallel B-sheet, B-turn, and random coil portions of the polypeptide [11]. With the increasing use being made of such agents in the pharmaceutical industry, it... 

Aromatic Side Chains. The usual dogma is that while far UV CD spectra of proteins reflect the secondary structure of proteins, the near UV CD spectra indicate changes in tertiary structure. This viewpoint arises from the fact that near UV CD spectra arise from aromatic groups in a fixed geometry relative to the peptide backbone and surrounding chromophores. Loss of tertiary structure would disrupt this ordering and lead to a diminished or altered near UV CD spectrum. 

The vibrational spectra of molecules dissolved in water are different in significant ways from the spectra of these molecules in the gas phase. The study of water solution spectra is particularly important for molecules of biological significance because their structure and properties are often determined by the presence or absence of water. Computational techniques have been developed that relate computationally determined structure and associated properties such as force constants to experimental information such as vibrational frequencies. Experimental vibrational studies have been used to elucidate information about such problems as the secondary structure of proteins in water solution. A brief review of the computational and experimental techniques is presented. Our work, which builds on the essential combination of theoretical and experimental information, is then reviewed to outline our ideas about using computational studies to investigate the complicated problems of amino acids and proteins in water solution. Finally some suggestions are presented to show how computational techniques can enhance the use of experimental techniques, such as isotopic substitution for the study of complicated molecules. 

Fu, K., Griebenow, K., Hsieh, L., Klibanov, A. M., and Langer, R. (1999), FTIR characterization of the secondary structure of proteins encapsulated within PLGA microspheres, /. Controlled Release, 58, 357-366. 

UV resonance Raman spectroscopy (UVRR), Sec. 6.1, has been used to determine the secondary structure of proteins. The strong conformational frequency and cross section dependence of the amide bands indicate that they are sensitive monitors of protein secondary structure. Excitation of the amide bands below 210 nm makes it possible to selectively study the secondary structure, while excitation between 210 and 240 nm selectively enhances aromatic amino acid bands (investigation of tyrosine and tryptophan environments) (Song and Asher, 1989 Wang et al., 1989, Su et al., 1991). Quantitative analysis of the UVRR spectra of a range of proteins showed a linear relation between the non-helical content and a newly characterized amide vibration referred to as amide S, which is found at 1385 cm (Wang et al., 1991). 

Byler, D. M. and Susi, H. Examination of the secondary structure of proteins by deconvolved FTIR spectra. Biopolymers 25 469-487, 1986. 

In addition to the alpha, beta, and random coil motifs in the secondary structure of protein depicted... 

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