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Ligand Binding Sites

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Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
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Cooperative Allosteric Transitions01:58

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Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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Most chemical reactions in cells require enzymes—biological catalysts that speed up the reaction without being consumed or permanently changed. They reduce the activation energy needed to convert the reactants into products. Enzymes are proteins, that usually work by binding to a substrate—a reactant molecule that they act upon.
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Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
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Selección conformacional inversa en la unión lipídica a las proteínas

Amélie Bacle1, Pavel Buslaev2,3, Rebeca Garcia-Fandino4,5

  • 1Laboratoire Coopératif "Lipotoxicity and Channelopathies - ConicMeds", Université de Poitiers, 1 rue Georges Bonnet, Poitiers 86000, France.

Journal of the American Chemical Society
|September 1, 2021
PubMed
Resumen

Los grupos de cabezas de lípidos exhiben una amplia gama de conformaciones, no solo unas pocas estructuras rígidas. Esta flexibilidad conformacional permite que los lípidos se unan efectivamente a varias biomoléculas, incluidas las proteínas, el ARN y los medicamentos.

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Área de la Ciencia:

  • Bioquímica y nanobiotecnología
  • Biofísica molecular

Sus antecedentes:

  • Los grupos de lípidos en las membranas y las nanopartículas median las interacciones con las biomoléculas.
  • Comprender las conformaciones de los grupos de lípidos es crucial para campos como la nanobiotecnología (por ejemplo, los portadores de vacunas de ARNm).
  • Los estudios anteriores carecían de datos experimentales sobre conjuntos conformacionales de grupos de lípidos en condiciones fisiológicas.

Objetivo del estudio:

  • Determinar los conjuntos conformacionales de los principales grupos de lípidos en condiciones biológicamente relevantes.
  • Para investigar si los grupos de cabezas de lípidos adoptan algunas estructuras rígidas o un espectro continuo de conformaciones.
  • Explorar las implicaciones de la flexibilidad de los grupos de lípidos para las interacciones biomoleculares.

Principales métodos:

  • Experimentos combinados de resonancia magnética nuclear (RMN) en estado sólido y simulaciones de dinámica molecular (DM) (Proyecto de lípidos RMN).
  • Analizado cuatro tipos de lípidos clave bajo diversas condiciones.
  • Se examinaron 894 estructuras lipídicas ligadas a proteínas del Banco de Datos de Proteínas (PDB).

Principales resultados:

  • Los grupos de lípidos muestran una amplia gama de conformaciones superpuestas en membranas neutras y cargadas.
  • La química del grupo de cabezas influye en la distribución de probabilidad de las conformaciones, no en el rango en sí.
  • Los lípidos se unen a las proteínas en diversas conformaciones, independientemente de la química del grupo principal.

Conclusiones:

  • Los grupos de lípidos poseen una amplia flexibilidad conformacional.
  • Los lípidos utilizan esta flexibilidad para seleccionar conformaciones apropiadas para unirse a diversos sitios de proteínas.
  • El modelo de selección conformacional inversa propuesto se aplica a las interacciones de lípidos con proteínas, medicamentos, ARN y virus.