Polypeptide structures

Two of the three single bonds involved in each unit are flexible, and their detailed conformation dictates overall polypeptide structures and (ultimately) function. The amide bond is generally assumed to be rigid. Why (See also Chapter 10, Problem 1.)... 

Three ferredoxins were isolated and characterized fromZ). africanus. The proteins are dimers of subunits with a molecular mass of circa 6 kDa. D. africanus Fdl contains a single [4Fe-4S] center bound to a polypeptide structure of 60 amino acids with only 4 cysteines. This is the minimal requirement for [4Fe-4S] cluster binding. D. africanus Fdll is a minor component, not so well characterized, and seems to contain a [4Fe-4S] center (68, 69). Fdlll of this strain is a dimer containing 61 amino acids and 7 cysteine residues per subunit. The protein contains a [3Fe-4S] and a [4Fe-4S] cluster (70-72). 

Historically, research on polypeptide structure, whether by experimental or computational means, has focused on the folded state only. This is because an array of methods exist for detailed investigation of the folded state of a polypeptide, and because the folded state is commonly the functionally active one. There are, however, two scenarios in which a full characterization of the unfolded state becomes as essential as the determination of the folded conformation. The first is in the study of... 

Peptides and proteins are composed of amino acids polymerized together through the formation of peptide (amide) bonds. The peptide bonded polymer that forms the backbone of polypeptide structure is called the a-chain. The peptide bonds of the a-chain are rigid planar units formed by the reaction of the oc-amino group of one amino acid with the a-carboxyl group of another (Figure 1.1). The peptide bond possesses no rotational freedom due to the partial double bond character of the carbonyl-amino amide bond. The bonds around the oc-carbon atom, however, are true single bonds with considerable freedom of movement. 

Figure 1.1 Rigid peptide bonds link amino acid residues together to form proteins. Other bonds within the polypeptide structure may exhibit considerable freedom of rotation.

Figure 1.13 The a-chain structure of alkaline phosphatase illustrates the complex nature of polypeptide structure within proteins (Kim and Wyckoff, 1991).

At the two extremes, lysine is observed as the amino acid most accessible on the surface of proteins while cysteine is the least exposed amino acid. The inaccessibility of cysteine probably stems from the fact that disulfides are typically buried within the polypeptide structure of proteins, whether they are intrachain or interchain in nature, and proteins rarely contain many reduced cysteine thiols. 

Recently, a second or alternative nitrogenase has been isolated from Azotobacter vinelandii (21) and Azotobacter chroococcum (22) that contains vanadium as opposed to molybdenum. The MoFe and VFe nitrogenase proteins from A. vinelandii (called Av and. 4vl , respectively) are known to have different polypeptide structures and it obviously of interest to know to what extent the cluster composition is conserved. Variable temperature MCD studies of the as isolated and thionine oxidized proteins provided a convenient means of addressing this question. 

One protein kinase, namely cAMP-dependent protein kinase, has been extensively studied to relate primary polypeptide structure... 

NMR and kinetic studies have been conducted with the hope of providing more details about the position and conformation of the polypeptide substrate in cAMP-dependent protein kinase. These have served to narrow down the possible spatial relationships between enzyme bound ATP and the phosphorylated serine. Thus, a picture of the active site that is consistent with the available data can be drawn (12,13,66,67). Although these studies have been largely successful at eliminating some classes of secondary polypeptide structure such as oi-hellces, 6-sheets or an obligatory 6-turn conformation 66), the precise conformation of the substrate is still not known. The data are consistent with a preference for certain 6-turn structures directly Involving the phosphorylated serine residue. However, they are also consistent with a preference or requirement for either a coil structure or some nonspecific type of secondary structure. Models of the ternary active-site complexes based on both the coil and the, turn conformations of one alternate peptide substrate have" been constructed (12). These two models are consistent with the available kinetic and NMR data. 

It is secreted by acidophil cells. Human growth hormone has a single straight chain polypeptide structure containing two intramolecular disulphide bridges and is composed of 188 amino acids. 

The ubiquitous electrochemical behavior of ferrocene and its relative chemical stability have made this organometallic complex a useful group for the preparation of redox-active devices. The incorporation of ferrocene-modified amino acids into larger polypeptide structures can therefore lead to electrochemically active de novo designed proteins. In addition, the attachment of ferrocene derivatives to peptides make them electroactive and eligible to electrochemical detection. Hence, it is not surprising that the first synthesis of a ferrocene-modified amino acid dates back to the 1950s. 

The synthetic polyamino acids are convenient models for chemical studies of proteins since they have the extended polypeptide structure of the proteins but are free from the complications which arise in the proteins from the large number of different side chains. The work described here has been confined to the water-soluble polyamino acids poly-D,L-alanine (PDLA), poly-a,L-glutamic acid (PGA), poly-a,D-glutamic acid, and poly-a,L-lysine, and the polyimino acid, poly-L-proline. 

As already discussed in Chapter 11, there are more than 10 000 protein structures known but only about 30 3D structure types. This might be traced to a limited number of possible stable polypeptide structures but most probably reflects the evolutionary history of the diversity of proteins. There are structural motifs which repeat themselves in a multitude of enzymes which are otherwise neither structurally nor functionally related, such as TIM barrel proteins, four-helix bundle proteins, Rossmann folds, or a/j3-folds of hydrolases (Figure 16.1). 

Turns are segments between secondary structural elements and are defined as sites in a polypeptide structure where the peptidic chain reverses its overall... 

The MoFe proteins from a number of bacterial sources have been isolated. Their polypeptide structures are highly conserved and their inorganic components (2 Mo 30 Fe 32 S2 per molecule) are all very similar [3], The MoFe proteins from A. vinelandii, Clostridium pasteuranium, and Klebsiella pneumoniae are denoted by Avl, Cp 1, and Kp 1, respectively. Early Mossbauer spectroscopy demonstrated [12] that the Fe atoms were probably present as clusters, and a wide range of spectroscopic techniques have been used in attempts to understand the structures of these clusters. 

A photochromic polymer containing azobenzene units has also been prepared by modification of a naturally occurring microbial poly(E-L-lysine) (Scheme 5, Structure IX), and investigated by means of absorption and circular dichroism spectroscopy.1431 The structure of this polymer, however, does not correspond to those of polypeptides, which are poly(amide)s of a-amino acids, and therefore the results cannot be discussed in terms of the typical polypeptide structures (a-helix, P-structure, random coil) and their standard CD spectra. 

Fu, R. and Cross, T. A. (1999) Solid-state nuclear magnetic resonance investigation of protein and polypeptide structure. Annu. Rev. Biophys. Biomol. Struct. 28, 235-268. 

It should be emphasized that these parameters should not be regarded as fixed, i.e. polypeptide structures are not necessarily rigid. However, departures from these values (and from the assumed planar trans conformation of the backbone amide group) can be taken care of by introducing appropriate energy terms to allow for such departures (see Section VE). 

A comparison of the maps of Figs. 15 and 16 illustrates similar additional steric restrictions on a poly-L-alanine chain, as one passes from a dipeptide (Fig. 15) to helical structures (Fig. 16). Further discussion of steric effects in small polypeptide structures can be found in the recent review of Ramachandran and Sasisekharan (1968). 

The next example of the mechanical properties of a standard polypeptide structure is that of silk, which is composed of extended (1 sheets. The stress-strain curve for drag silk of the spider (Figure 6.3) shows an ultimate tensile strength (UTS) of about 800MPa, a modulus of about 7.0 GPa, and a strain at failure of about 30%.The value of the UTS and modulus appears to be higher than that of collagen as we show in Chapter 7 after correction for orientation effects and other complications the values for collagen are... 

---