Distance-constraint approach to higher-order structures of globular proteins with empirically determined distances between amino acid residues

1991 ◽  
Vol 10 (2) ◽  
pp. 233-243 ◽  
Author(s):  
Hiroshi Wako ◽  
Yasushi Kubota

A number of facts relating to proteins suggest that the polypeptides in native protein are in a folded state (Astbury 1933, 1934; Astbury and Street 1930, 1931; Pryde 1931; Wrinch 1936 a , b , c , 1937 a ; Langmuir, Schaefer and Wrinch 1937). The type of folding must be such as to imply the possibility of the regular and orderly arrangement of hundreds 01 amino-acid residues which to some extent at least is independent of the particular residues in question. We propose therefore to formulate all types of folding which are geometrically possible. Each hypothesis in turn can then be tested in two ways. We may consider its plausibility in itself: and having developed its implications to the farthest possible point, we may test it against known facts by ad hoc experiments. At present two types of folding have been suggested—by means of cyclol links (Wrinch 1936 a , b , c , 1937 a ; Langmuir, Schaefer and Wrinch 1937; Astbury 1936 a , b , c ; Frank, 1936) and by means of hydrogen bonds (Jordan Lloyd 1932; Jordan Lloyd and Marriott 1933; Mirsky and Pauling 1936; Wrinch and Jordan Lloyd 1936). The search for other types of folding is being continued. So far it has not proved possible to discard either theory on the grounds that the type of link postulated is out of the question. It is there­ fore very desirable to test these theories by means of their implications. Accordingly, on this occasion we consider (Wrinch 1937 b , c ) whether the cyclol theory can stand the test of the body of facts relating to the “globular” proteins, established by Svedberg and his collaborators (Svedberg and others 1929, 1930 a , b , 1934 a , b , 1935).


2010 ◽  
Vol 192 (7) ◽  
pp. 1853-1864 ◽  
Author(s):  
Xin Guo ◽  
Li Huang

ABSTRACT Replication proteins encoded by nonconjugative plasmids from the hyperthermophilic archaea of the order Sulfolobales show great diversity in amino acid sequence. We have biochemically characterized ORF735, a replication protein from pSSVi, an integrative nonconjugative plasmid from Sulfolobus solfataricus P2. We show that ORF735 is a DNA helicase of superfamily 3. It unwound double-stranded DNA (dsDNA) in a 3′-to-5′ direction in the presence of ATP over a wide range of temperatures, from 37°C to 75°C, and possessed DNA-stimulated ATPase activity. ORF735 existed in solution as a salt-stable dimer and was capable of assembling into a salt-sensitive oligomer that was significantly larger than a hexamer in the presence of a divalent cation (Mg2+) and an adenine nucleotide (ATP, dATP, or ADP) or its analog (ATPγS or AMPPNP). Both N-terminal and C-terminal portions of ORF735 (87 and 160 amino acid residues, respectively, in size) were required for protein dimerization but dispensable for the formation of the higher-order oligomer. The protein unwound DNA only as a large oligomer. Yeast two-hybrid and coimmunoprecipitation assays revealed that ORF735 interacted with the noncatalytic subunit of host primase. These findings provide clues to the functional role of ORF735 in pSSVi DNA replication.


2009 ◽  
Vol 24 (2) ◽  
pp. 180-191 ◽  
Author(s):  
R. BHASKARAN ◽  
P.K. PONNUSWAMY

Biomolecules ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 64 ◽  
Author(s):  
Galina S. Nagibina ◽  
Ksenia A. Glukhova ◽  
Vladimir N. Uversky ◽  
Tatiana N. Melnik ◽  
Bogdan S. Melnik

Directed stabilization of globular proteins via substitution of a minimal number of amino acid residues is one of the most complicated experimental tasks. This work summarizes our research on the effect of amino acid substitutions on the protein stability utilizing the outputs of the analysis of intrinsic disorder predisposition of target proteins. This allowed us to formulate the basis of one of the possible approaches to the stabilization of globular proteins. The idea is quite simple. To stabilize a protein as a whole, one needs to find its "weakest spot" and stabilize it, but the question is how this weak spot can be found in a query protein. Our approach is based on the utilization of the computational tools for the per-residue evaluation of intrinsic disorder predisposition to search for the "weakest spot" of a query protein (i.e., the region(s) with the highest local predisposition for intrinsic disorder). When such "weakest spot" is found, it can be stabilized through a limited number of point mutations by introducing order-promoting residues at hot spots, thereby increasing structural stability of a protein as a whole. Using this approach, we were able to obtain stable mutant forms of several globular proteins, such as Gαo, GFP, ribosome protein L1, and circular permutant of apical domain of GroEL.


2002 ◽  
Vol 184 (15) ◽  
pp. 4270-4276 ◽  
Author(s):  
Marcus Eccleston ◽  
Reem Ahmed Ali ◽  
Richard Seyler ◽  
Janet Westpheling ◽  
Justin Nodwell

ABSTRACT We have demonstrated that the bldB gene of Streptomyces coelicolor is required for the formation of aerial hyphae and the synthesis of antibiotics. We also found that BldB forms a higher-order complex (most likely a dimer) and that amino acid residues 20 to 78 are important for this interaction. This region is conserved in the BldB family, suggesting that dimer formation may be a common feature of these proteins.


Science ◽  
1985 ◽  
Vol 229 (4716) ◽  
pp. 834-838 ◽  
Author(s):  
G. Rose ◽  
A. Geselowitz ◽  
G. Lesser ◽  
R. Lee ◽  
M. Zehfus

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