Re: beta barrels

Daniel Dubois (ddubois@rsvs.ulaval.ca)
Fri, 10 Mar 1995 16:43:20 -0500

>BUT, isn't a beta-barrel a parallel beta-sheet????
>AND, isn't a beta-barrel a common folding pattern????
>FURTHERMORE, as a beta-barrel satisfies the hydrogen-bonding of all
>the beta-strands, isn't it more stable than an anti-parallel sheet
>with the same number of strands????
>
>-Pete
>

Here some clues that might help you:

For the basic definition of beta sheet:

"Beta strands can interact in two ways to form a pleated sheet. Either the
amino acids in the aligned beta strands can all run in the same biochemical
direction, amino terminal to carboxy terminal, in which case the sheet is
described as PARALLEL, or the amino acids in successive strands can have
alternating directions, amino terminal to carboxy terminal followed by
carboxy terminal to amino terminalfollowed by amino terminal to carboxy
terminal, and so on, in wich case the sheet is called ANTIPARALLEL. Each of
the two forms has a distinctive pattern of hydrogen bonding. The
antiparallel beta sheet has narrowly spaced hydrogen bond pairs that
alternate with widely spaced pairs. Parallel beta sheets have evenly spaced
hydrogen bonds that angle across between the beta strands. Within both types
of beta sheets all possible main chain hydrogen bonds are formed, except for
the two flanking strands of the beta sheet that only have
only one neighboring beta strand."(From Branden and Tooze, p. 15 and 16)

For the beta barrel (wich is a antiparallel beta sheet)

"The simplest topology is obtained if each successive beta strand is added
adjacent to the previous strand until the barrel is closed and the last
strand is joined by hydrogen bonds to the first strand. These are called
up-and-down beta sheets or barrels. The arrangement of beta strands is
similar to that in the alpha/beta barrel structures except that here the
strands are antiparallel and all the connections are hairpins."(From Branden
and Tooze, p. 60)

Branden, C. and Tooze, J. Introduction to protein structure
Garland Publishing, Inc. New York and London, 1991 (302 pages)

Good luck :-).
----------------------------------------------------------------------------
Daniel Y. Dubois Tel. 418 656-2131 #6273
Pav. Charles-Eugene Marchand Fax. 418 656-7176
Departement de Biochimie E-mail: ddubois@rsvs.ulaval.ca
Universite Laval BioMOO nickname: DanDubois
Ste-Foy, Quebec, Canada
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