Skip to main content

Calculating the Secrets of Life Contributions of the Mathematical Sciences to Molecular Biology (1995) / Chapter Skim
Currently Skimming:


Pages 248-253

The Chapter Skim interface presents what we've algorithmically identified as the most significant single chunk of text within every page in the chapter.
Select key terms on the right to highlight them within pages of the chapter.


From page 248...
... The converse of this statement offers a recipe for protein structure prediction: if a "new" protein sequence is recognizably similar to the sequence of a protein of known structure, then it should be possible to approximate the "new" structure by threading the sequence of the "new" protein through the "old" structure guided by the sequence alignment. The key step is to accurately align the new sequence with the known structure.
Read the entire page →
From page 249...
... The likelihood that any residue wait be mutated into another residue could depend on the mechanisms for somatic mutation as well as on the implications of the substitution for the stability or catalytic efficiency of a protein that is, it could depend both on mutation and selection. We need to determine the likelihood of all possible interchanges between the 20 natural amino acids, that is, create a 20 x 20 transition matrix for a Markov process (although sequence evolution is not strictly Markovian)
Read the entire page →
From page 250...
... Turn regions are accommodating, but the midges of secondary structure elements are more problematic. Smith has asserted that the gap penalty should be equal to
Read the entire page →
From page 251...
... building (Greer, 1990; Chothia et al., 1989; Jones and Thirup, 1986; Bruccoleri and Karplus, 1987; Ponder and Richards, 1987; Wilson et al., 19934. One method is based on using secondary structure segments to create a molecular scaffold, thereby decomposing the problem.
Read the entire page →
From page 252...
... They took hemerythrin and an immunogIobulin domain, two proteins with entirely different secondary and tertiary structure. The hemerythrin sequence was forced into the immunogiobuTin structure and vice versa.
Read the entire page →
From page 253...
... For this and other reasons, fourth-generation potential functions are being developed that include a solvent accessibility term as a method for implicitly incorporating proteinsolvent interactions. Another issue in evaluating proposed protein structures is the treatment of electrostatic interactions (GiTson and Honig, 1986~.
Read the entire page →

Key Terms

  • secondary structure
  • tertiary structure
  • protein structure
  • free energy
  • protein structures

  • amino acid
  • structure prediction
  • amino acids
  • dynamic programming
  • structure elements

  • multiple sequence
  • protein folding
  • common ancestor
  • protein sequences
  • potential functions

  • programming algorithm
  • protein chain
  • electrostatic interactions
  • accessible surface
  • sequentially distant

  • existing potential
  • protein sequence
  • sequence alignment


    • This material may be derived from roughly machine-read images, and so is provided only to facilitate research.
    More information on Chapter Skim is available.