This article has been reviewed according to Science X's editorial process and policies. Editors have highlighted the following attributes while ensuring the content's credibility: For decades, scientists have understood proteins primarily through two defining features: their amino acid sequence and their three-dimensional structure. This framework has driven major advances in biology, biotechnology and medicine, culminating in recent artificial intelligence tools capable of predicting protein structures with remarkable accuracy.
Yet a fundamental challenge remains: Even when a protein's sequence and structure are known, predicting its function, interactions and behavior often remains difficult. An international team of researchers from Japan, Finland, Italy and the United States now reports evidence that part of this missing information may lie in an often-overlooked component of proteins: the highly organized water surrounding them. In a study published in Nature Communications, the team provides the first direct three-dimensional visualization of sequence-dependent hydration architectures surrounding peptide assemblies at subnanometer resolution using advanced three-dimensional atomic force microscopy (3D-AFM).
The findings reveal that water near peptide and protein surfaces is not simply a passive solvent. Instead, it forms highly organized, multilayered structures whose organization is dictated by the underlying amino acid sequence and surface chemistry. These hydration architectures extend multiple layers from the peptide surface and contain distinct structural signatures associated with hydrophobic, polar, aromatic and charged amino acid residues.
The researchers propose that these hydration structures are not merely consequences of the protein's presence but are an integral part of protein identity and function. This has led them to introduce a new concept: the protein superstructure, defined as the protein together with its uniquely organized hydration architecture. "Our findings suggest that proteins cannot be fully understood by sequence and structure alone," said Prof.
Mehmet Sarikaya of the University of Washington. "The highly specific hydration architecture organized by a protein appears to be part of its functional identity. We define this integrated protein-water entity as the protein superstructure." Water is essential to virtually every biological process.
Proteins fold in water, recognize molecular partners, catalyze reactions and function exclusively in aqueous environments. Scientists have long known that hydration influences protein folding, stability, molecular recognition and enzymatic activity. However, directly observing the three-dimensional molecular organization of hydration water locally around proteins has remained one of the major challenges in molecular biology and biophysics.
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