I'm new to biology field, so I'm learning all kinds of biochemistry knowledge for a bioinformatics project. I've found a few definitions of secondary structure online. For example, I found this brief definition here:

A structure of a biological molecule characterized by the local folding within the biopolymer as a result of hydrogen bonding (within the biopolymer).

What does "local folding" mean here? More specifically, what does "local" in this context refer to? Thanks in advanced.

  • $\begingroup$ Please provide a link to your quote. We need to be able to see it in context. $\endgroup$ – David Apr 7 '17 at 21:58

The most common examples of secondary structure in proteins are alpha helices and beta sheets, and the most important distinction between secondary and tertiary structure is that a single protein can have multiple "local structures", alpha helices and beta sheets, within its complete global structure. In contrast, a protein cannot have multiple "global structures" by definition.

In other words, a local structure can occur multiple times within a protein, while a global structure by definition can only occur once, and describes the complete shape of the protein.

  • $\begingroup$ Ok, so it means a local segment of the global structure? And because secondary structure do not specify the exact position of an atom, it is just a general template to represent what it is? And therefore, secondary structure do not specify the function of that segment? $\endgroup$ – Lingbo Tang Apr 7 '17 at 17:11
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    $\begingroup$ Secondary structures don't have specified positions in a protein, they can occur almost anywhere depending on the protein. However, secondary structures often do have important functions. For example, alpha helices are useful for proteins binding to DNA and for proteins crossing cell membranes. $\endgroup$ – mxwsn Apr 7 '17 at 17:16
  • $\begingroup$ It's interesting to know that the secondary structure has such a generic function. Could you also briefly explain why the secondary structures can occur almost anywhere? $\endgroup$ – Lingbo Tang Apr 7 '17 at 17:20
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    $\begingroup$ There are likely a few structural constraints for where secondary structures can occur, to allow for energetically stable folding and bending, but I'm not too familiar with them. Secondary structures are very common though - why? probably no better answer than simply evolution found them useful. It's fairly straightforward to construct secondary structures, you just need to ensure that your linear sequence of amino acids has certain bioechmical properties, like a lot of MALEK: en.wikipedia.org/wiki/Alpha_helix#Amino-acid_propensities $\endgroup$ – mxwsn Apr 7 '17 at 17:27
  • $\begingroup$ This is very helpful for me to understand what's going on because I've been reading some papers using these parameters to predict the secondary structure. $\endgroup$ – Lingbo Tang Apr 7 '17 at 17:33

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