Alexander V. Efimov

The organization of potato virus X coat proteins in virus particles studied by tritium planigraphy and model building

Potato virus X particles containing the intact, undegraded Ps form of the coat protein and particles containing the in situ degraded Pf form of the coat protein, which is devoid of 19-21 amino acids from the N-terminus, were bombarded with thermally activated tritium atoms, and the intramolecular distribution of the tritium label was studied. The tritium planigraphy revealed that the N-terminal region of the coat protein is the most accessible region for both type of PVX particles. The C-terminal region of the coat protein in the intact virus particles is almost inaccessible to the hot tritium atoms, whereas in Pf particles this region becomes available for the tritium label. A model of PVX coat protein tertiary structure was built, taking into account the predicted secondary structure of the protein, the principles of packing alpha-helices and beta-structure in globular proteins, and known biochemical, immunological, and tritium bombardment data. In the model one beta-sheet consisting of beta-strands at regions 1-12, 14-22, and 24-33 flanks the molecule and forms the outside surface of the PVX particles.

STRUCTURAL TREES FOR PROTEIN SUPERFAMILIES

Structural trees for large protein superfamilies, such as β proteins with the aligned β sheet packing, β proteins with the orthogonal packing of α helices, two‐layer and three‐layer α/β proteins, have been constructed. The structural motifs having unique overall folds and a unique handedness are taken as root structures of the trees. The larger protein structures of each superfamily are obtained by a stepwise addition of α helices and/or β strands to the corresponding root motif, taking into account a restricted set of rules inferred from known principles of the protein structure. Among these rules, prohibition of crossing connections, attention to handedness and compactness, and a requirement for α helices to be packed in α‐helical layers and β strands in β layers are the most important. Proteins and domains whose structures can be obtained by stepwise addition of α helices and/or β strands to the same root motif can be grouped into one structural class or a superfamily. Proteins and domains found within branches of a structural tree can be grouped into subclasses or subfamilies. Levels of structural similarity between different proteins can easily be observed by visual inspection. Within one branch, protein structures having a higher position in the tree include the structures located lower. Proteins and domains of different branches have the structure located in the branching point as the common fold. Proteins 28:241–260, 1997.

Patterns of loop regions in proteins

The commonly occurring loop structures and their sequence patterns for the key hydrophobic, hydrophilic and glycine residues are described. There is a restricted number of the loop motifs consisting of three to six residues that occur most often and these small standard structures can be considered as elements of irregular regions. A short loop has, as a rule, conformation of one of the small standard structures and a longer loop can be represented as a combination of two or more small standard structures.

Common structural motifs in small proteins and domains

The high frequency of occurrence of the definite folding units in unrelated proteins and the fact that many small proteins are merely composed of the folding units indicate that these units can fold into unique structures per se and can be nuclei or ‘ready building blocks’ in protein folding.

Favoured structural motifs in globular proteins.

While many different structural motifs have been observed to recur within globular proteins, only some of the motifs exhibit unique handedness and a unique overall fold.

Complementary packing of α-helices in proteins

The packing of α‐helices in proteins is restricted by both the principle of close packing and the chemical nature of side chains. As a result, (1) α‐helical surfaces forming the interface should be complementary to each other, (2) hydrophobic stripes of the α‐helices should fit together like pieces of a jigsaw puzzle, and (3) buried polar side chains (if there are any) should be arranged in a complementary fashion.

A structural tree for proteins containing 3β-corners

A structural tree for β‐proteins with predominantly orthogonal β‐sheet packing has been constructed. The 3β‐corner, a structural motif that recurs in proteins of this class, is taken as a root structure of the tree. The 3β‐corner can be represented as a triple‐stranded β‐sheet folded on to itself so that its two β‐β‐hairpins are packed approximately orthogonally in different layers and the central strand bends by ∼90° in a right‐handed direction when passing from one layer to the other. The larger protein structures are obtained by stepwise addition of β‐strands to the root 3β‐corner taking into account a restricted set of rules inferred from known principles of protein structure. The protein structures that can be obtained in this way are grouped into one structural class and those found in branches of the structural tree into subclasses.

Relationship between intramolecular hydrogen bonding and solvent accessibility of side-chain donors and acceptors in proteins.

This study shows that intramolecular hydrogen bonding in proteins depends on the accessibility of donors and acceptors to water molecules. The frequency of occurrence of H‐bonded side chains in proteins is inversely proportional to the solvent accessibility of their donors and acceptors. Estimates of the notional free energy of hydrogen bonding suggest that intramolecular hydrogen‐bonding interactions of buried and half‐buried donors and acceptors can contribute favorably to the stability of a protein, whereas those of solvent‐exposed polar atoms become less favorable or unfavorable.

Super-secondary structures involving triple-strand β-sheets

Triple‐strand β‐sheets having up‐and‐down topology are widespread in proteins and occur in two forms denoted here as S‐like and Z‐like β‐sheets. In many cases they are included in super‐secondary structures of higher order. A number of such structures is described in this paper. An important feature of these super‐secondary structures is that they have a unique handedness. Another feature is that some of them only involve S‐like β‐sheets and others only Z‐like β‐sheets.

A structural tree for proteins containing S‐like β‐sheets

A structural tree for proteins and domains containing S‐like β‐sheets has been constructed. An S‐like β‐sheet is taken as a starting structure in modelling or as a root structure of the tree. Larger structures are obtained by a stepwise addition of β‐strands and/or α‐helices to the root S‐like β‐sheet in accordance with a restricted set of rules inferred from known principles of protein structure. Applications of the structural tree to structure comparison, protein classification and protein folding are described.