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Amino acids03:42

Amino acids

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Amino acids are the monomers that comprise proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom, or the alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and to a hydrogen atom. Every amino acid also has another atom or group of atoms bonded to the central atom known as the R group. There are 20 common amino acids present in proteins, each with a different R group. Variation in the amino acid sequence is responsible for...
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Amino Acid Catabolism01:18

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Microorganisms rely on proteins as an essential carbon and energy source, particularly in environments with limited polysaccharides or lipids. However, proteins are too large to cross the plasma membrane unaided, necessitating enzymatic degradation. Microbes secrete extracellular proteases and peptidases that hydrolyze proteins into peptides, which can then be transported across the membrane. Once inside the cell, intracellular proteases degrade these peptides into free amino acids, which...
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Amino Acid Biosynthetic Pathways01:29

Amino Acid Biosynthetic Pathways

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Amino acid biosynthesis is essential for cell growth, protein synthesis, and metabolic regulation. Cells generate essential and non-essential amino acids from metabolic intermediates to sustain vital biological functions. These intermediates originate from key metabolic pathways: glycolysis, the tricarboxylic acid (TCA) cycle, and the pentose phosphate pathway. Important precursors include α-ketoglutarate, pyruvate, oxaloacetate, phosphoenolpyruvate, and erythrose-4-phosphate, which...
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Phase II Reactions: Sulfation and Conjugation with α-Amino Acids01:19

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Sulfation and α-amino acid conjugation are two critical biotransformation reactions in drug metabolism. Sulfation, a phase II biotransformation reaction, involves adding a polar sulfate group to a drug, enhancing its water solubility and promoting excretion. This process can either co-occur with or occur independently of glucuronidation. Nonmicrosomal sulfotransferase enzymes catalyze the process. The reaction involves 3'-phosphoadenosine-5'-phosphosulfate or PAPS coenzyme...
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Nucleophilic Acyl Substitution of Carboxylic Acid Derivatives01:15

Nucleophilic Acyl Substitution of Carboxylic Acid Derivatives

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Nucleophilic acyl substitution is an important class of substitution reactions involving a nucleophile and an acyl compound, such as carboxylic acids and their derivatives. In these reactions, the leaving group attached to the acyl group is substituted by a nucleophile. The general mechanism proceeds via two steps.
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Polyprotic Acids

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Acids are classified by the number of protons per molecule that they can give up in a reaction. Acids such as HCl, HNO3, and HCN that contain one ionizable hydrogen atom in each molecule are called monoprotic acids. Their reactions with water are:
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Updated: Feb 12, 2026

Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers
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RECURRENCIA: Identificación de sustituciones recurrentes de aminoácidos a partir de alineamientos de secuencias

Elizabeth H J Robbins1, Yi Liu1, Steven Kelly1

  • 1Department of Biology, University of Oxford, South Parks Road, Oxford, OX1 3RB, United Kingdom.

Molecular biology and evolution
|February 11, 2026
PubMed
Resumen

RECUR identifica las sustituciones recurrentes de aminoácidos en secuencias biológicas, cruciales para comprender la evolución y las enfermedades. Este método detecta con precisión la evolución recurrente generalizada en las proteínas del pico del SARS-CoV-2, particularmente en la interfaz hACE2.

Palabras clave:
Adaptación de la adaptación.La evolución convergente es una evolución convergente.Alineación de secuencias múltiples.La evolución paralela de la evolución es paralela.La filogenia es la filogenia.Evolución recurrente recurrente.El SARS-CoV-2 es una glicoproteína de superficie.

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Área de la Ciencia:

  • Biología evolutiva Biología evolutiva.
  • La genómica es la genómica.
  • Biología estructural Biología estructural.

Sus antecedentes:

  • Los cambios evolutivos recurrentes en las secuencias biológicas son vitales para comprender los fenotipos, la resistencia a los antibióticos y las enfermedades.
  • La identificación de estas sustituciones recurrentes ayuda a identificar las alteraciones genéticas causantes.

Objetivo del estudio:

  • Introducir RECUR, un nuevo método computacional para detectar sustituciones recurrentes de aminoácidos en grandes alineaciones de secuencias múltiples.
  • Evaluar la precisión y la robustez de RECUR utilizando datos biológicos simulados y del mundo real.

Principales métodos:

  • Desarrollo de RECUR, un algoritmo rápido, fácil de usar y escalable para identificar las sustituciones recurrentes de aminoácidos.
  • Validación de la precisión de RECUR (100%) en datos simulados y su robustez contra errores de inferencia de árbol.
  • Aplicación de RECUR para analizar las secuencias de proteínas de la glicoproteína (S) de superficie del SARS-CoV-2.

Principales resultados:

  • RECUR logró una precisión del 100% en la detección de sustituciones recurrentes en historias evolutivas simuladas.
  • Se identificó una evolución recurrente generalizada en las proteínas S del SARS-CoV-2, enriquecidas en la subunidad S1 y en la interfaz de unión hACE2.
  • Las sustituciones recurrentes se agotaron en la interfaz trímerica de la proteína S, con efectos de estabilidad variables en la interfaz hACE2.

Conclusiones:

  • RECUR es una herramienta altamente precisa y robusta para identificar eventos evolutivos recurrentes en secuencias biológicas.
  • La evolución recurrente en la proteína S del SARS-CoV-2, especialmente en la interfaz hACE2, sugiere un equilibrio entre la unión al receptor y la evasión inmune.
  • Los hallazgos destacan la utilidad de RECUR en el estudio de la evolución y adaptación viral.