Definition and research guide
This page combines a MeSH definition, publication statistics and selected research abstracts. It is a starting point for reading the literature, not a medical textbook or a systematic evidence review.
Content available: 4 complete abstracts (595 words), 10 references. Full article text is not stored or reproduced here; follow the PMID, DOI or PMC links to read the original sources and their access terms.
Definition
The naturally occurring or experimentally induced replacement of one or more amino acids in a protein with another. If a functionally equivalent amino acid is substituted, the protein may retain wild-type activity. Substitution may also diminish, enhance, or eliminate protein function. Experimentally induced substitution is often used to study enzyme activities and binding site properties.
Definition: NLM Medical Subject Headings (MeSH) scope note (Public domain (U.S. National Library of Medicine); attribution requested). View the MeSH record.
Also known as: Amino Acid Substitutions; Substitution, Amino Acid; Substitutions, Amino Acid.
Where it fits in the MeSH classification
- Broader topics
- Protein Engineering; Mutagenesis
- See also
- Mutagenesis, Site-Directed; Mutation, Missense
Related concepts
- Amino Acids
Research landscape
PubMed indexes 44,800 records tagged with the MeSH heading “Amino Acid Substitution” (counts retrieved 2026-10-29). 3,075 of them (6.9%) were published from 2020 onward, and the busiest period so far is 2000-2009 with 20,948 records.
Reviews account for 1,122 records (2.5%) and meta-analyses for 271. Randomized controlled trials number 97 (0.2%) as a share of all records on the topic. Randomized trials make up only a small share of this literature, so much of what is known comes from laboratory, observational or descriptive work.
Show the data
| Period | Records |
|---|---|
| through 1999 | 2,880 |
| 2000-2009 | 20,948 |
| 2010-2019 | 17,897 |
| 2020 onward | 3,075 |
Publication-type chart data
| Type | Records | Share |
|---|---|---|
| Reviews | 1,122 | 2.5% |
| Meta-analyses | 271 | 0.6% |
| Randomized controlled trials | 97 | 0.2% |
Method: PubMed query "Amino Acid Substitution"[MeSH Terms] with publication-type and date filters, retrieved 2026-10-29.
Reading the evidence in genetics and genomics
Genetic findings vary widely in strength. A variant linked to a condition in one study may not replicate in other ancestries, and most common variants have small effects that are meaningful only in aggregate. Studies of rare, high-impact variants can support strong causal claims about a gene, while association studies describe statistical links that need functional and independent replication. Check the sample size, the ancestry of participants, whether results were replicated, and whether a laboratory or clinical outcome was actually measured.
Evidence from open-access studies
These open-access studies come from PubMed’s best-match results for this heading (papers whose main topic it is), ranked here by citation count, with one recent addition. Each abstract is reproduced in full under its recorded open licence so that you can read the authors’ own words. They illustrate the literature; they are not a systematic summary of it. Citation counts measure attention, not reliability or clinical benefit.
| Study / authors | Year | Source label / design | Europe PMC citations | Licence / source |
|---|---|---|---|---|
| Structure-based design of prefusion-stabilized SARS-CoV-2 spikes | 2020 | Research article Design not recorded in structured metadata | 1,353 | cc by PMID 32703906 · DOI · PMC7402631 |
| Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity | 2021 | Research article Design not recorded in structured metadata | 876 | cc by PMID 33275900 · DOI · PMC7674007 |
| Inferring the molecular and phenotypic impact of amino acid variants with MutPred2 | 2020 | Research article Design not recorded in structured metadata | 705 | cc by PMID 33219223 · DOI · PMC7680112 |
| AI-Based D-Amino Acid Substitution for Optimizing Antimicrobial Peptides to Treat Multidrug-Resistant Bacterial Infection | 2026 | Research article Design not recorded in structured metadata | 7 | cc by PMID 41532671 · DOI · PMC12915103 |
Structure-based design of prefusion-stabilized SARS-CoV-2 spikes [1]
Abstract reading summary — source excerpts
- Opening excerpt
- The coronavirus disease 2019 (COVID-19) pandemic has led to accelerated efforts to develop therapeutics and vaccines.
- Closing excerpt
- High-yield production of a stabilized prefusion spike protein will accelerate the development of vaccines and serological diagnostics for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
- Interpretation limits
- Verbatim excerpts from the authors’ abstract; the closing excerpt may describe a finding, limitation or recommendation. Design, population, effect size and uncertainty have not been independently extracted or appraised. Read the complete abstract and linked paper before interpreting the findings.
Read complete abstract (144 words)
The coronavirus disease 2019 (COVID-19) pandemic has led to accelerated efforts to develop therapeutics and vaccines. A key target of these efforts is the spike (S) protein, which is metastable and difficult to produce recombinantly. We characterized 100 structure-guided spike designs and identified 26 individual substitutions that increased protein yields and stability. Testing combinations of beneficial substitutions resulted in the identification of HexaPro, a variant with six beneficial proline substitutions exhibiting higher expression than its parental construct (by a factor of 10) as well as the ability to withstand heat stress, storage at room temperature, and three freeze-thaw cycles. A cryo-electron microscopy structure of HexaPro at a resolution of 3.2 angstroms confirmed that it retains the prefusion spike conformation. High-yield production of a stabilized prefusion spike protein will accelerate the development of vaccines and serological diagnostics for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
Abstract reproduced from the open-access article under the recorded cc by licence; © the authors. PMID 32703906 · DOI · PMC7402631
Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity [2]
Abstract reading summary — source excerpts
- Opening excerpt
- Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect.
- Closing excerpt
- Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant.
- Interpretation limits
- Verbatim excerpts from the authors’ abstract; the closing excerpt may describe a finding, limitation or recommendation. Design, population, effect size and uncertainty have not been independently extracted or appraised. Read the complete abstract and linked paper before interpreting the findings.
Read complete abstract (147 words)
Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant.
Abstract reproduced from the open-access article under the recorded cc by licence; © the authors. PMID 33275900 · DOI · PMC7674007
Inferring the molecular and phenotypic impact of amino acid variants with MutPred2 [3]
Abstract reading summary — source excerpts
- Opening excerpt
- Identifying pathogenic variants and underlying functional alterations is challenging.
- Closing excerpt
- We argue that mechanism-driven studies of human inherited disease have the potential to significantly accelerate the discovery of clinically actionable variants.
- Interpretation limits
- Verbatim excerpts from the authors’ abstract; the closing excerpt may describe a finding, limitation or recommendation. Design, population, effect size and uncertainty have not been independently extracted or appraised. Read the complete abstract and linked paper before interpreting the findings.
Read complete abstract (150 words)
Identifying pathogenic variants and underlying functional alterations is challenging. To this end, we introduce MutPred2, a tool that improves the prioritization of pathogenic amino acid substitutions over existing methods, generates molecular mechanisms potentially causative of disease, and returns interpretable pathogenicity score distributions on individual genomes. Whilst its prioritization performance is state-of-the-art, a distinguishing feature of MutPred2 is the probabilistic modeling of variant impact on specific aspects of protein structure and function that can serve to guide experimental studies of phenotype-altering variants. We demonstrate the utility of MutPred2 in the identification of the structural and functional mutational signatures relevant to Mendelian disorders and the prioritization of de novo mutations associated with complex neurodevelopmental disorders. We then experimentally validate the functional impact of several variants identified in patients with such disorders. We argue that mechanism-driven studies of human inherited disease have the potential to significantly accelerate the discovery of clinically actionable variants.
Abstract reproduced from the open-access article under the recorded cc by licence; © the authors. PMID 33219223 · DOI · PMC7680112
AI-Based D-Amino Acid Substitution for Optimizing Antimicrobial Peptides to Treat Multidrug-Resistant Bacterial Infection [4]
Abstract reading summary — source excerpts
- Opening excerpt
- D-amino acid substitution provides an effective strategy for optimizing antimicrobial peptides (AMPs) by enhancing their stability.
- Closing excerpt
- Overall, our study established an AI-based framework for D-amino acid substitution in AMPs, enabling the efficient discovery of potent and stable candidates with enhanced clinical translation potential.
- Interpretation limits
- Verbatim excerpts from the authors’ abstract; the closing excerpt may describe a finding, limitation or recommendation. Design, population, effect size and uncertainty have not been independently extracted or appraised. Read the complete abstract and linked paper before interpreting the findings.
Read complete abstract (154 words)
D-amino acid substitution provides an effective strategy for optimizing antimicrobial peptides (AMPs) by enhancing their stability. However, the absence of universal rules renders traditional screening methods time-consuming and labor-intensive, potentially leading to reduced or complete loss of activity. Here, we curated a D-amino acid-substituted AMP dataset from published literature and databases. We then developed ADAPT, an AI-based tool for predicting the functional impact of D-amino acid substitutions, and integrated it into a high-throughput screening pipeline for AMP optimization. Of the variants obtained through this pipeline, 80% exhibited enhanced antibacterial activity. Among these, dR2-1 showed exceptional broad-spectrum antimicrobial activity, reduced toxicity, and substantially improved stability. Mechanistic studies confirmed a membrane-targeting antibacterial mode of action. Furthermore, we engineered a hydrogel delivery system that effectively treated cutaneous infections in mice. Overall, our study established an AI-based framework for D-amino acid substitution in AMPs, enabling the efficient discovery of potent and stable candidates with enhanced clinical translation potential.
Abstract reproduced from the open-access article under the recorded cc by licence; © the authors. PMID 41532671 · DOI · PMC12915103
Key reviews and meta-analyses
The most cited review-type papers among PubMed’s best-match results for this heading, listed with bibliographic details only. Follow the links for the full text and access terms.
- Research article Phaser.MRage: automated molecular replacement [5]
- Research article Screening for amino acid substitutions in the Candida albicans Erg11 protein of azole-susceptible and azole-resistant clinical isolates: new substitutions and a review of the literature [6]
- Research article Update of the Drug Resistance Mutations in HIV-1 [7]
- Research article Challenges and complexities in estimating both the functional impact and the disease risk associated with the extensive genetic variation in human DNA repair genes [8]
- Research article Molecular evolution of animal antimicrobial peptides: widespread moderate positive selection [9]
- Research article Gly972Arg variant in the insulin receptor substrate-1 gene and association with Type 2 diabetes: a meta-analysis of 27 studies [10]
References
- Hsieh CL, Goldsmith JA, Schaub JM, DiVenere AM, Kuo HC, Javanmardi K, et al.. Structure-based design of prefusion-stabilized SARS-CoV-2 spikes. . 2020. PMID 32703906 · DOI · PMC7402631
- Volz E, Hill V, McCrone JT, Price A, Jorgensen D, O'Toole Á, et al.. Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. . 2021. PMID 33275900 · DOI · PMC7674007
- Pejaver V, Urresti J, Lugo-Martinez J, Pagel KA, Lin GN, Nam HJ, et al.. Inferring the molecular and phenotypic impact of amino acid variants with MutPred2. . 2020. PMID 33219223 · DOI · PMC7680112
- Zhao Y, Kong Q, Gong H, Li L, Fu J, Wan B, et al.. AI-Based D-Amino Acid Substitution for Optimizing Antimicrobial Peptides to Treat Multidrug-Resistant Bacterial Infection. . 2026. PMID 41532671 · DOI · PMC12915103
- Bunkóczi G, Echols N, McCoy AJ, Oeffner RD, Adams PD, Read RJ. Phaser.MRage: automated molecular replacement. Acta Crystallogr D Biol Crystallogr. 2013. PMID 24189240 · DOI · PMC3817702
- Morio F, Loge C, Besse B, Hennequin C, Le Pape P. Screening for amino acid substitutions in the Candida albicans Erg11 protein of azole-susceptible and azole-resistant clinical isolates: new substitutions and a review of the literature. Diagn Microbiol Infect Dis. 2010. PMID 20226328 · DOI
- Johnson VA, Brun-Vezinet F, Clotet B, Gunthard HF, Kuritzkes DR, Pillay D, et al.. Update of the Drug Resistance Mutations in HIV-1. Top HIV Med. 2008. PMID 19106428
- Mohrenweiser HW, Wilson DM, Jones IM. Challenges and complexities in estimating both the functional impact and the disease risk associated with the extensive genetic variation in human DNA repair genes. Mutat Res. 2003. PMID 12714187 · DOI
- Tennessen JA. Molecular evolution of animal antimicrobial peptides: widespread moderate positive selection. J Evol Biol. 2005. PMID 16313451 · DOI
- Jellema A, Zeegers MP, Feskens EJ, Dagnelie PC, Mensink RP. Gly972Arg variant in the insulin receptor substrate-1 gene and association with Type 2 diabetes: a meta-analysis of 27 studies. Diabetologia. 2003. PMID 12819898 · DOI
About this article
- Sources
- NLM Medical Subject Headings (definition, synonyms); NCBI PubMed (counts, identifiers); Europe PMC (open-access abstracts and citation counts).
- Verification
- Every reference was resolved against PubMed on 2026-10-31; title, year and DOI matched.
- Review state
- automated source verified; no human expert review has been recorded yet.
- Version
- 1, last updated 2026-10-29.
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Evidence strength
EvidenceHelix's computed view of the study designs behind this topic: how common meta-analyses, randomized trials and reviews are, how recent the literature is, and a plain-language reading. It describes the design mix of the literature. It is not a quality appraisal of any study, and it is not medical advice.