Editing Hydrophobic effect (section)

== Folding of macromolecules ==

In the case of protein folding, the hydrophobic effect is important to understanding the structure of proteins that have hydrophobic [[amino acid]]s (such as [[valine]], [[leucine]], [[isoleucine]], [[phenylalanine]], [[tryptophan]] and [[methionine]]) clustered together within the protein. Structures of globular proteins have a hydrophobic core in which hydrophobic [[side chains]] are buried from water, which stabilizes the folded state. Charged and [[chemical polarity|polar]] side chains are situated on the solvent-exposed surface where they interact with surrounding water molecules. Minimizing the number of hydrophobic side chains exposed to water is the principal driving force behind the folding process,<ref name="Pace">{{cite journal | vauthors = Pace CN, Shirley BA, McNutt M, Gajiwala K | title = Forces contributing to the conformational stability of proteins | journal = FASEB J. | volume = 10 | issue = 1 | pages = 75–83 | date = 1 January 1996 | pmid = 8566551 | url = http://www.fasebj.org/cgi/reprint/10/1/75 | doi=10.1096/fasebj.10.1.8566551| doi-access = free | s2cid = 20021399 | url-access = subscription }}</ref><ref name="pmid24187909">{{cite journal
 |vauthors=Compiani M, Capriotti E
 |title=Computational and theoretical methods for protein folding
 |journal=Biochemistry
 |volume=52
 |issue=48
 |pages=8601–24
 |date=Dec 2013
 |pmid=24187909
 |doi=10.1021/bi4001529
 |url=http://biofold.org/emidio/pages/documents/papers/Compiani_Biochemistry2013.pdf
 |url-status=dead
 |archive-url=https://web.archive.org/web/20150904053433/https://biofold.org/emidio/pages/documents/papers/Compiani_Biochemistry2013.pdf
 |archive-date=2015-09-04
}}</ref><ref name="pmid7846023">{{Cite journal
| pmid = 7846023
| arxiv = cond-mat/9406071
| year = 1994
| last1 = Callaway
| first1 = David J. E.
| title = Solvent-induced organization: a physical model of folding myoglobin
| journal = Proteins: Structure, Function, and Bioinformatics
| volume = 20
| issue = 1
| pages = 124–138
| doi = 10.1002/prot.340200203
| bibcode = 1994cond.mat..6071C
| s2cid = 317080
}}</ref> although formation of hydrogen bonds within the protein also stabilizes protein structure.<ref name="Rose">{{cite journal | vauthors = Rose GD, Fleming PJ, Banavar JR, Maritan A | title = A backbone-based theory of protein folding | journal = Proc. Natl. Acad. Sci. U.S.A. | volume = 103 | issue = 45 | pages = 16623–33 | year = 2006 | pmid = 17075053 | pmc = 1636505 | doi = 10.1073/pnas.0606843103 | bibcode = 2006PNAS..10316623R | doi-access = free }}</ref><ref name="Karp2009">{{cite book|author=Gerald Karp
|title=Cell and Molecular Biology: Concepts and Experiments
|url=https://books.google.com/books?id=arRGYE0GxRQC&pg=PA128
|year=2009|publisher=John Wiley and Sons
|isbn=978-0-470-48337-4|pages=128–}}</ref>

The [[energy|energetics]] of [[DNA]] tertiary-structure assembly were determined to be driven by the hydrophobic effect, in addition to [[Watson–Crick base pairing]], which is responsible for sequence selectivity, and [[Stacking (chemistry)|stacking interactions]] between the aromatic bases.<ref>{{cite book | author = Gilbert HF | title = Basic concepts in biochemistry: a student's survival guide | year = 2001 | publisher = McGraw-Hill | location = Singapore | isbn = 978-0071356572 | edition = 2nd, International | page = [https://archive.org/details/basicconceptsinb00hira/page/9 9] | url-access = registration | url = https://archive.org/details/basicconceptsinb00hira/page/9 }}</ref><ref>{{cite book |vauthors=Ho PS, van Holde KE, Johnson WC, Shing P | title = Principles of physical biochemistry | year = 1998 | publisher = Prentice-Hall | location = Upper Saddle River, N.J. | isbn = 978-0137204595 | page = 18 | quote = See also thermodynamic discussion pages 137-144 }}</ref>