Protein loop conformations

Q Zheng, R Rosenfeld, S Vajda, C DeLisi. Determining protein loop conformation using scahng-relaxation techniques. Protein Sci 2 1242-1248, 1993. 

Q. Zheng, R. Rosenfeld, S. Vajda, C. DeLisi. Determining protein loop conformation using scaling-relaxation techniques. Prot. Science. 1993, 2, 1242-1248. 

RM Fine, H Wang, PS Shenkm, DL Yarmush, C Levmthal. Predicting antibody hypervariable loop conformations. II Minimization and molecular dynamics studies of MCP603 from many randomly generated loop conformations. Proteins 1 342-362, 1986. 

RNA structures, compared to the helical motifs that dominate DNA, are quite diverse, assuming various loop conformations in addition to helical structures. This diversity allows RNA molecules to assume a wide variety of tertiary structures with many biological functions beyond the storage and propagation of the genetic code. Examples include transfer RNA, which is involved in the translation of mRNA into proteins, the RNA components of ribosomes, the translation machinery, and catalytic RNA molecules. In addition, it is now known that secondary and tertiary elements of mRNA can act to regulate the translation of its own primary sequence. Such diversity makes RNA a prime area for the study of structure-function relationships to which computational approaches can make a significant contribution. 

The main advantage of NMR spectroscopy is its use with proteins in solution. In consequence, rather than obtaining a single three-dimensional structure of the protein, the final result for an NMR structure is a set of more or less overlying structures which fulfill the criteria and constraints given particularly by the NOEs. Typically, flexibly oriented protein loops appear as largely diverging structures in this part of the protein. Likewise, two distinct local conformations of the protein are represented by two differentiated populations of NMR structures. Conformational dynamics are observable on different time scales. The rates of equilibration of two (or more) substructures can be calculated from analysis of the line shape of the resonances and from spin relaxation times Tj and T2, respectively. 

Fig. 5.19. GTP and GDP structures of transducin. The Ga,t subunit of transducin possesses—in contrast to Ras protein and to other small regulatory GTPases —an a-hehcal domain that hides and closes the G-nucleotide binding pocket. The conformational changes that accompany the transition from the inactive G t GDP form (a) into the active G t GTP form (b), are restricted to three structural sections that are known as switches I, II and III. Switch I includes the link of the a-helical domain with P2, switch II affects in particular hehx a2, and switch III, the pS—a3 loop. Switch III includes a sequence that is characteristic for the a-subunits of the heterotrimeric G-proteins. The conformational changes of switches II and III affect structural sections that are assumed to be binding sites for the effector molecule adenylyl cyclase (AC) and the y-subunit of cGMP-dependent phosphodiesterase (PDEy), based on mutation experiments and biochemical investigations. MOLSKRIPT representation according to Krauhs, (1991).

Kettleborough, C.A., Saldanha, J., Heath, V.J., et al. (1991). Humanization of a mouse monoclonal-antibody by CDR-grafting—The importance of framework residues on loop conformation. Protein Eng., 4, 773-783. 

Another example of a quantal repeat—but with considerable variation in sequence—is seen in the keratin-associated proteins (KAPs). In sheep, these display pentapeptide and decapeptide consensus repeats of the form G—G—Q—P—S/T and C-C-Q/R—P—S/T—C/S/T—C—Q—P/T—S, respectively (Parry et al., 1979). Some of the positions, as indicated by the presence of a consensus sequence, contain residues that occur much more frequently than others, but the absolute conservation of a residue in any position is not observed. The decapeptide consists of a pair of five-residue repeats closely related, but different to that displayed by the pentapeptide. Although the repeats have an undetermined structure, the similarity of the repeat to a sequence in snake neurotoxin suggests that the pentapeptides will adopt a closed loop conformation stabilized by a disulphide bond between cysteine residues four apart (Fig. 5 Fraser et al., 1988 Parry et al, 1979). Relative freedom of rotation about the single bond connecting disulphide-bonded knots would give rise to the concept of a linear array of knots that can fold up to form a variety of tertiary structures. The KAPS display imperfect disulphide stabilization of knots and have interacting... 

Canonical Loop Conformation Examples Found in Extracellular Hydrolases, Toxins, Cytokines and Viral Proteins. 

R. M. Fine, H. Wang, P. S. Shenkin, D. L. Yarmush, and C. Levinthal, Proteins Struct. Fund. Genet., 1, 342 (1986). Predicting Antibody Hypervariable Loop Conformations. II. Minimization and Molecular Dynamics Studies of MCPC603 from Many Randomly Generated Loop Conformations. 

The first step, as alluded to above, is the development of possible loop conformations which connect the regions of secondary structure The loops which do not fit into the well-defined category of a-helices or (1-sheets have been fairly well characterized using the data base of proteins for which the three-dimensional structure is known [15,16], The identification of specific loop conformations provides insight into the possible orientations, or at least provides limitations on the possible orientations, of the various secondary structural elements. The second step is then analysis of the array of amino acids within the secondary structural elements with attention to the environment in which the amino acids would be found. It is clear that a cluster of hydrophobic amino acids would not likely be projecting into the aqueous solution, and more likely projecting into the core of the protein. This analysis provides additional restrictions to the number of possible arrangements in which the secondary structural elements may be found. 

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