Essay: The Hydrogen Bond in Molecular Physiology

The Hydrogen Bond in Molecular Physiology

Author:  Adisha Kariyawasam BSc Molecular Biophysics, MScIT, PGCE (PCET), BCS

Originally written Autumn 1992, BSc (Hons) Molecular Biophysics, University of Leeds

Republished and expanded 2025

Preface (2025 Edition)

This second essay in the Molecular Biophysics series was written in 1992 while studying protein structure and macromolecular interactions at the University of Leeds. The hydrogen bond - once viewed as a minor chemical curiosity - was being recognised as the cornerstone of molecular structure and biological stability.

In this essay, I examined the central claim by Linus Pauling that hydrogen bonding might prove “more significant for physiology than any other single structural feature.” The work set out to test this claim by exploring the role of hydrogen bonds in proteins, membranes, nucleic acids, and connective tissue.

The Hydrogen Bond in Molecular Physiology

“It has been recognised that hydrogen bonds restrain protein molecules to their native configurations, and I believe that as the methods of structural chemistry are further applied to physiological problems it will be found that the significance of the hydrogen bond for physiology is greater than that of any other single structural feature.”
(Pauling, 1939 in The Nature of the Chemical Bond)

 

Introduction

Pauling’s statement was both visionary and provocative. To evaluate its accuracy, one must ask three key questions:

1. What experimental techniques reveal hydrogen bonds in biological molecules?

2. To what extent do these bonds restrain molecular motion and structure?

3. What physiological roles do such interactions perform?

Techniques for Studying Hydrogen Bonds

• X-ray Diffraction shows that strong hydrogen bonds shorten the expected van der Waals distances by 0.2–0.3 Å.

• Nuclear Magnetic Resonance (NMR) detects characteristic shifts in proton resonance when hydrogen bonding occurs.

• Infra-red (IR) Spectroscopy reveals frequency shifts in stretching and bending modes (e.g. C=O and N–H) that mark the presence of hydrogen bonds.

Together these methods provide a three-dimensional and dynamic picture of bonding within and between macromolecules.

Proteins and the Role of Hydrogen Bonds

Hydrogen bonds are fundamental to protein conformation. Water molecules at a protein’s surface form extensive hydrogen-bonded networks, while interior residues maintain tight intra-chain bonding.

On a protein’s surface, polar side-chains can create or disrupt hydrogen bonds, altering reactivity. The best-known example is haemoglobin, in which hydrogen bonds influence oxygen affinity.

• In oxyhaemoglobin, breaking specific hydrogen bonds allows oxygen binding.

• In deoxyhaemoglobin, hydrogen bonds involving histidines 58 and 87 stabilise the low-oxygen form.

Mutations such as Haemoglobin Thionville (Vasseur et al., 1987) modify hydrogen-bonding at subunit interfaces, demonstrating how small structural changes can affect oxygen transport and stability.

Membranes and Ion Transport

Hydrogen bonds are also vital in membrane physiology. Ionophores such as valinomycin employ rearrangements of six carbonyl oxygen atoms, held by internal hydrogen bonds, to complex potassium ions. This dynamic bonding enables selective ion transport across membranes - an essential feature of bioenergetics.

In transmembrane proteins, regular hydrogen-bonding patterns stabilise α-helices and β-sheets that traverse lipid bilayers. Loss of these interactions can cause chain bending or pore collapse, compromising membrane integrity.

Helices and Structural Frameworks

Collagen

The collagen triple helix is stabilised by inter-chain hydrogen bonds involving hydroxyproline and hydroxylysine. Vitamin C deficiency prevents hydroxylation, weakening these bonds and leading to collagen degradation - a molecular explanation for scurvy.

DNA Double Helix

The DNA double helix, the molecule of heredity, owes its stability to hydrogen-bonded base pairs—adenine with thymine, guanine with cytosine - complemented by hydrophobic stacking. The pairing rules encode genetic fidelity.

Gene Regulation

Hydrogen bonds also guide protein – DNA recognition. In bacteriophage λ, the CRO repressor binds to its operator region through a specific pattern of hydrogen-bond donors and acceptors within the DNA’s major groove. This precise bonding determines whether the phage enters lysogenic or lytic pathways.

Molecular Recognition and Immunology

Hydrogen bonding governs the specificity of antibody–antigen interactions. In the FAB D1.3–lysozyme complex, six complementarity-determining regions (CDRs) form a dense network of hydrogen bonds that position antigen residues for recognition.

A single substitution - replacing glutamine 121 with histidine in Californian quayle lysozyme - breaks one crucial hydrogen bond, lowering binding energy by ≈ 40 kJ mol⁻¹ and abolishing affinity. This striking sensitivity exemplifies the precision of hydrogen bonding in immune recognition.

Carbohydrates and the Extracellular Matrix

Hydrogen bonds stabilise the polysaccharide frameworks of the extracellular matrix. In glycoproteins and proteoglycans, extensive hydrogen bonding confers both elasticity and hydration. Components such as hyaluronate form helical structures whose viscosity arises from hydrogen-bonded water networks.

Fibrous proteins (collagen, elastin, fibronectin, laminin) interweave with these polysaccharides, forming the molecular scaffold of tissues. Even cellulose, the structural polymer of plants, derives its rigidity from hydrogen bonds between adjacent chains - arguably biology’s most widespread structural motif.

Conclusion: Is Pauling Vindicated?

The examples above confirm that hydrogen bonds pervade every level of biological organisation—from enzyme catalysis to connective tissue mechanics. While other forces (ionic, van der Waals, disulphide bridges) also contribute, none rival the ubiquity of the hydrogen bond.

Pauling’s prediction has been amply fulfilled: hydrogen bonding is not merely significant but central to molecular physiology. As later commentators have suggested (Chang, 1981), if anything, its importance may once have been underestimated.

Afterword (2025 Reflection)

Modern structural biology has deepened our understanding of hydrogen bonding beyond Pauling’s imagination. Cryo-EM, ultrafast spectroscopy, and quantum simulations now reveal the fleeting vibrations and proton transfers that animate molecular life.

Hydrogen bonds are no longer seen as static connections but as dynamic conduits of energy and information. From protein folding algorithms to enzyme design and DNA nanotechnology, the “hydrogen-bond code” continues to shape the frontier of molecular medicine.

References (Harvard Format)

• Chang, R. (1981) Physical Chemistry with Applications to Biological Systems. New York: Macmillan.

• Kendrew, J.C. (1963) ‘Structural Biology: The New Landscape’, Scientific American, 208 (5), pp. 96–108.

• Pauling, L. (1939) The Nature of the Chemical Bond. Ithaca: Cornell University Press.

• Vasseur, C., et al. (1987) ‘Haemoglobin Thionville: Functional and structural analysis’, Journal of Biological Chemistry, 262 (18), pp. 12682–12691.

• Chang, R. (1981) Physical Chemistry with Applications to Biological Systems, 2nd edn. New York: Macmillan.

Appendix 1 – Glossary of Key Terms

Term	Definition
α-Helix / β-Sheet	Common protein secondary structures stabilised by hydrogen bonds between backbone atoms.
Antibody (Immunoglobulin)	A protein produced by B cells that recognises specific antigens.
Base Pairing	Hydrogen-bonded interaction between nucleotide bases in DNA and RNA.
Collagen	A fibrous structural protein whose triple-helix stability depends on inter-chain hydrogen bonding.
Hydrogen Bond	A weak electrostatic attraction between a hydrogen atom covalently bonded to an electronegative atom (e.g. O or N) and another electronegative atom with a lone pair.
Ionophore	A molecule that facilitates ion transport across membranes via reversible binding.
Lysozyme	An enzyme that hydrolyses bacterial cell-wall polysaccharides; a model protein for studying molecular recognition.
NMR Spectroscopy	Technique exploiting magnetic properties of nuclei to study molecular structure.
Proteoglycan	A glycoprotein rich in polysaccharides forming part of connective tissue matrices.
Scurvy	Disease caused by vitamin C deficiency, leading to impaired collagen hydroxylation and weakened hydrogen bonding.

Appendix 2 – Short Biographies of Scientists Mentioned (Alphabetical by Surname)

Chang, Raymond (1939–2017)

Chinese-American physical chemist and textbook author. His Physical Chemistry with Applications to Biological Systems (1981) brought thermodynamics and bonding concepts into biochemical education, influencing generations of molecular scientists.

Engström, Lars

Swedish biochemist known for work on cell ultrastructure with James B. Finean. Their 1969 book Biological Ultrastructure helped establish structural approaches to cell biology.

Finean, James B. (1913–1987)

British biophysicist who elucidated membrane structure through electron microscopy and diffraction studies. His collaboration with Engström linked macroscopic tissue structure to molecular organisation.

Kendrew, John Cowdery (1917–1997)

British structural biologist who, with Max Perutz, solved the first protein structures (myoglobin and haemoglobin) by X-ray crystallography. He shared the 1962 Nobel Prize in Chemistry.

Pauling, Linus Carl (1901–1994)

American chemist and molecular biologist awarded the 1954 Nobel Prize in Chemistry and the 1962 Nobel Peace Prize. His concept of the chemical bond and prediction of α-helices and β-sheets formed the foundation of modern structural biology.

Vasseur, Claude

French biochemist whose late-1980s work on mutant haemoglobins (e.g. Haemoglobin Thionville) demonstrated how altered hydrogen bonding affects oxygen transport and allosteric regulation.

Disclaimer

The views, interpretations, and reflections expressed in this essay are those of the author A. Kariyawasam and do not necessarily represent the positions or opinions of staff at the University of Leeds or any affiliated institution.