Polypeptide Research Articles

Human erythrocytes under stress. Spectroscopic fingerprints of known oxidative mechanisms and beyond

In this work, we investigated the oxidative stress-related biochemical alterations in red blood cells (RBCs) and their membranes with the use of spectroscopic techniques. We aimed to show their great advantage for the in situ detection of lipid classes and secondary structures of proteins without the need for their extraction in the cellular environment. The exposition of the cells to peroxides, t-butyl hydroperoxide (tBOOH) or hydrogen peroxide (H2O2) led to different degradation processes encompassing the changes in the composition of membranes and structural modifications of hemoglobin (Hb). Our results indicated that tBOOH is generally a stronger oxidizing agent than H2O2 and this observation was congruent with the activity of superoxide and glutathione peroxidase. ATR-FTIR and Raman spectroscopies of membranes revealed that tBOOH caused primarily the partial loss and peroxidation of the lipids resulting in loss of the integrity of membranes. In turn, both peroxides induced several kinds of damage in the protein layer, including the partial decrease of their content and irreversible aggregation of spectrin, ankyrin, and membrane-bound globin. These changes were especially pronounced on the membrane surface where stress conditions induced the formation of β-sheets and intramolecular aggregates, particularly for tBOOH. Interestingly, nano-FTIR spectroscopy revealed the lipid peroxidative damage on the membrane surface in both cases. As far as hemoglobin was concerned, tBOOH and H2O2 caused the increase of the oxyhemoglobin species and conformational alterations of its polypeptide chain into β-sheets. Our findings confirm that applied spectroscopies effectively track the oxidative changes occurring in the structural components of red blood cells and the simplicity of conducting measurements and sample preparation can be readily applied to pharmacological and clinical studies.

Modification of Protein Micelles by Limited Hydrolysis of Peptide Bonds: A Model of the Sequential Degradation of β-Casein Micelles

A model for the degradation of β-casein micelles with the limited hydrolysis of trypsin-specific peptide bonds was proposed. A sequential mechanism of the degradation of micelles and assembly of peptide nanoparticles from the fragments of a β-casein polypeptide chain was considered. The degradation kinetics was studied by numerical modeling, taking into account the formation of intermediate components of different sizes and peptide nanoparticles, which are more difficult to hydrolyze with trypsin. The simulation results are consistent with the experimental data previously obtained by atomic force microscopy, FTIR spectroscopy, and light scattering.

Structure of a novel form of phosphopantetheine adenylyltransferase from Klebsiella pneumoniae at 2.59Å resolution.

Phosphopantetheine adenylyltransferase (EC. 2.7.7.3, PPAT) catalyzes the penultimate step of the multistep reaction in the coenzyme A (CoA) biosynthesis pathway. In this step, an adenylyl group from adenosine triphosphate (ATP) is transferred to 4'-phosphopantetheine (PNS) yielding 3'-dephospho-coenzyme A (dpCoA) and pyrophosphate (PPi). PPAT from strain C3 of Klebsiella pneumoniae (KpPPAT) was cloned, expressed and purified. It was crystallized using 0.1M HEPES buffer and PEG10000 at pH 7.5. The crystals belonged to tetragonal space group P41212 with cell dimensions of a = b = 72.82Å and c = 200.37Å. The structure was determined using the molecular replacement method and refined to values of 0.208 and 0.255 for Rcryst and Rfree factors, respectively. The structure determination showed the presence of three crystallographically independent molecules A, B and C in the asymmetric unit. The molecules A and B are observed in the form of a dimer in the asymmetric unit while molecule C belongs to the second dimer whose partner is related by crystallographic twofold symmetry. The polypeptide chain of KpPPAT folds into a β/α structure. The conformations of the side chains of several residues in the substrate binding site in KpPPAT are significantly different from those reported in other PPATs. As a result, the modes of binding of substrates, phosphopantetheine (PNS) and adenosine triphosphate (ATP) differ considerably. The binding studies using fluorescence spectroscopy indicated a KD value of 3.45 × 10-4M for ATP which is significantly lower than the corresponding values reported for PPAT from other species.

Structural effects of charge destabilization and amino acid substitutions in amyloid fragments of CsgA

The most studied functional amyloid is the CsgA, major curli subunit protein, which is produced by numerous strains of Enterobacteriaceae. Although CsgA sequences are highly conserved, they exhibit species diversity, which reflects the specific evolutionary and functional adaptability of the major curli subunit. Herein, we performed bioinformatics analyses to uncover the differences in the amyloidogenic properties of the R4 fragments in Escherichia coli and Salmonella enterica and proposed four mutants for more detailed studies: M1, M2, M3, and M4. The mutated sequences were characterized by various experimental techniques, such as circular dichroism, ATR-FTIR, FT-Raman, thioflavin T, transmission electron microscopy and confocal microscopy. Additionally, molecular dynamics simulations were performed to determine the role of buffer ions in the aggregation process. Our results demonstrated that the aggregation kinetics, fibril morphology, and overall structure of the peptide were significantly affected by the positions of charged amino acids within the repeat sequences of CsgA. Notably, substituting glycine with lysine resulted in the formation of distinctive spherically packed globular aggregates. The differences in morphology observed are attributed to the influence of phosphate ions, which disrupt the local electrostatic interaction network of the polypeptide chains. This study provides knowledge on the preferential formation of amyloid fibrils based on charge states within the polypeptide chain.

Engineered mRNA-ribosome fusions for facile biosynthesis of selenoproteins.

Ribosomes are often used in synthetic biology as a tool to produce desired proteins with enhanced properties or entirely new functions. However, repurposing ribosomes for producing designer proteins is challenging due to the limited number of engineering solutions available to alter the natural activity of these enzymes. In this study, we advance ribosome engineering by describing a novel strategy based on functional fusions of ribosomal RNA (rRNA) with messenger RNA (mRNA). Specifically, we create an mRNA-ribosome fusion called RiboU, where the 16S rRNA is covalently attached to selenocysteine insertion sequence (SECIS), a regulatory RNA element found in mRNAs encoding selenoproteins. When SECIS sequences are present in natural mRNAs, they instruct ribosomes to decode UGA codons as selenocysteine (Sec, U) codons instead of interpreting them as stop codons. This enables ribosomes to insert Sec into the growing polypeptide chain at the appropriate site. Our work demonstrates that the SECIS sequence maintains its functionality even when inserted into the ribosome structure. As a result, the engineered ribosomes RiboU interpret UAG codons as Sec codons, allowing easy and site-specific insertion of Sec in a protein of interest with no further modification to the natural machinery of protein synthesis. To validate this approach, we use RiboU ribosomes to produce three functional target selenoproteins in Escherichia coli by site-specifically inserting Sec into the proteins' active sites. Overall, our work demonstrates the feasibility of creating functional mRNA-rRNA fusions as a strategy for ribosome engineering, providing a novel tool for producing Sec-containing proteins in live bacterial cells.

Molecular Deformation Is a Key Factor in Screening Aggregation Inhibitor for Intrinsically Disordered Protein Tau.

Direct inhibitor of tau aggregation has been extensively studied as potential therapeutic agents for Alzheimer's disease. However, the natively unfolded structure of tau complicates the structure-based ligand design, and the relatively large surface areas that mediate tau-tau interactions in aggregation limit the potential for identifying high-affinity ligand binding sites. Herein, a group of isatin-pyrrolidinylpyridine derivative isomers (IPP1-IPP4) were designed and synthesized. They are like different forms of molecular "transformers". These isatin isomers exhibit different inhibitory effects on tau self-aggregation or even possess a depolymerizing effect. Our results revealed for the first time that the direct inhibitor of tau protein aggregation is not only determined by the previously reported conjugated structure, substituent, hydrogen bond donor, etc. but also depends more importantly on the molecular shape. In combination with molecular docking and molecular dynamics simulations, a new inhibition mechanism was proposed: like a "molecular clip", IPP1 could noncovalently bind and fix a tau polypeptide chain at a multipoint to prevent the transition from the "natively unfolded conformation" to the "aggregation competent conformation" before nucleation. At the cellular and animal levels, the effectiveness of the inhibitor of the IPP1 has been confirmed, providing an innovative design strategy as well as a lead compound for Alzheimer's disease drug development.

Use of Collagen in Cosmetic Products.

Collagen (CLG) belongs to the family of fibrillar proteins and is composed of left-handed α polypeptide chains, which, twisting around themselves and their axis, form a right-handed superhelix. In the chemical structure, it contains mainly proline, hydroxyproline, glycine, and hydroxylysine. It occurs naturally in the dermis in the form of fibers that provide the skin with proper density and elasticity. The review aimed to present the types of collagen protein, factors affecting its structure and its unusual role in the functioning of the human body. Also, an overview of cosmetic products containing collagen or its derivatives, the characteristics of the formulas of these products, and the effects of their use were presented. Throughout the market, there are many cosmetic and cosmeceutical products containing CLG. They are in the form of fillers administered as injections, belonging to the group of the oldest tissue fillers; products administered orally and for topical use, such as creams, gels, serums, or cosmetic masks. Analyzed studies have shown that the use of products with collagen or its peptides improves the general condition of the skin and delays the aging process by reducing the depth of wrinkles, improving hydration (in the case of oral preparations), reducing transepithelial water loss (TEWL), as well as improving skin density and elasticity. In addition, oral application of bioactive CLG peptides has shown a positive effect on the nails, reducing the frequency of their breakage.

Readthrough Activators and Nonsense-Mediated mRNA Decay Inhibitor Molecules: Real Potential in Many Genetic Diseases Harboring Premature Termination Codons.

Nonsense mutations that generate a premature termination codon (PTC) can induce both the accelerated degradation of mutated mRNA compared with the wild type version of the mRNA or the production of a truncated protein. One of the considered therapeutic strategies to bypass PTCs is their "readthrough" based on small-molecule drugs. These molecules promote the incorporation of a near-cognate tRNA at the PTC position through the native polypeptide chain. In this review, we detailed the various existing strategies organized according to pharmacological molecule types through their different mechanisms. The positive results that followed readthrough molecule testing in multiple neuromuscular disorder models indicate the potential of this approach in peripheral neuropathies.

Review: fish collagen: extraction, characterization and application in wound healing and drug delivery

Collagen is a natural protein presenting in the animal and human’s body. It is in natural fibrous and could be found in the connective tissue and flesh of mammal, approximately 25-35 wt.% of total human protein. Collagen is abundant in fibrous tissues such as: bones, cartilage, tendons, blood vessels, ligaments, skin, cornea, aortic disc and intestines. Fish collagen is currently being studied as a new biological substitute for collagen from animals. It extracted from by-products (scales, skins, bones, etc.) by biochemical or biological methods is safe, has high adsorption, high compatible. The factors influencing on the extraction process include temperature, time, concentration of ingredients, etc. The fish collagen is usually collagen type I with a fibril structure. Each unit of collagen is tropocollagen consisting of three polypeptide chains twisted together. Depending on the source of ingredients, the composition of aminoacids, denaturation temperature, the sequence of aminoacids, structure, morphology, molecular weight, extraction yield, etc. of obtained collagens are different. This paper reviews the extraction and characterization of fish collagen from products after fish processing by chemical or biochemical methods. The applications of fish collagen in wound healing and drug delivery are also reviewed.

Sulfur Switches for Responsive Peptide Materials.

There is considerable recent interest in the synthesis and development of peptide-based materials as mimics of natural biological assemblies that utilize proteins and peptides to form organized structures and develop beneficial properties. Due to their potential compatibility with living organisms, synthetic peptide materials are also being developed for applications such as cell grafting, therapeutic delivery, and implantable diagnostic devices. One desirable feature for such applications is the ability to design materials that can respond to stimuli by changes in their structure or properties under biologically relevant conditions. Peptide and protein assemblies can respond to stimuli, such as changes in temperature, solution pH, ions present in media, or interactions with other biomacromolecules. An exciting area of emerging research is focused on how biology uses the chemistry of sulfur-containing amino acids as a means to regulate biological processes. These concepts have been utilized and expanded in recent years to enable the development of peptide materials with readily switchable properties.The incorporation of sulfur atoms in polypeptides, peptides, and proteins provides unique sites that can be used to alter the physical and biological properties of these materials. Sulfur-containing amino acid residues, most often cysteine and methionine, are able to undergo a variety of selective chemical and enzyme-mediated reactions, which can be broadly characterized as redox or alkylation processes. These reactions often proceed under physiologically relevant conditions, can be reversible, and are significant in that they can alter residue polarity as well as conformations of peptide chains. These sulfur-based reactions are able to switch molecular and macromolecular properties of peptides and proteins in living systems and recently have been applied to synthetic peptide materials. Naturally occurring "sulfur switches" can be reversible or irreversible and are often triggered by enzymatic activity. Sulfur switches in peptide materials can also be triggered in vitro using oxidation/reduction and alkylation as well as photochemical reactions. The application of sulfur switches to peptide materials has greatly expanded the scope of these switches due to the ability to readily incorporate a wide variety of noncanonical sulfur-containing synthetic amino acids.Sulfur switches have been shown to provide considerable potential to reversibly alter peptide material properties under mild physiologically relevant conditions. An important molecular feature of sulfur-containing amino acid residues was found to be the location of sulfur atoms in the side chains. The variation of sulfur atom positions from the backbone by single bond lengths was found to significantly affect polypeptide chain conformations upon oxidation-reduction or alkylation/dealkylation reactions. With the successful adaptation of sulfur switches to peptide materials, future studies can explore how these switches affect how these materials interact with biological systems. This Account provides an overview of the different types of sulfur switch reactions found in biology and their properties and the elaboration of these switches in synthetic systems with a focus on recent developments and applications of reversible sulfur switches in peptide materials.

Reduction of antigenicity and emulsibility improvement of ovalbumin by dielectric-barrier discharge plasma treatment induced structure modification

The effects of Dielectric-Barrier Discharge (DBD) plasma treatment (40 kV, 1–4 min) on the structure, antigenicity and emulsibility of ovalbumin (OVA) were investigated. Plasma-induced structural changes of OVA were determined by SDS-PAGE, multi-spectroscopic, and LC-MS/MS analysis. Meanwhile, the reduction in antigenicity of OVA was evaluated by western blotting (WB) and enzyme-linked immunosorbent assay (ELISA) analysis. The results indicated effective elimination of the antigenicity of OVA was achieved after 4 min of plasma treatment. The immunoglobulin E (IgE) binding capacity of OVA was notably reduced by 90.80%, as evidenced by WB and ELISA analysis. Plasma-mediated oxidation led to the unfolding of OVA's structure, resulting in alterations to its conformational epitope, and the partial destruction of linear epitopes through polypeptide chain cleavage, thus contributing to the reduction in antigenicity. These findings were supported by the results of SDS-PAGE, multi-spectroscopic, and LC-MS/MS analysis. Furthermore, a significant increase (53%) in emulsifying ability and a one-fold improvement in emulsifying stability of OVA were achieved after 4 min of plasma treatment. The current study confirms that DBD plasma treatment not only reduces the allergenicity of OVA but also enhance its emulsibility through structural modification.

Crystal structure of the tegument protein UL82 (pp71) from human cytomegalovirus.

Human cytomegalovirus (HCMV) is an opportunistic pathogen that infects a majority of the world population. It may cause severe disease in immunocompromised people and lead to pregnancy loss or grave disabilities of the fetus upon congenital infection. For effective replication and lifelong persistence in its host, HCMV relies on diverse functions of its tegument protein UL82, also known as pp71. Up to now, little is known about the molecular mechanisms underlying the multiple functions of this crucial viral protein. Here, we describe the X-ray structure of full-length UL82 to a resolution of 2.7 Å. A single polypeptide chain of 559 amino acids mainly folds into three ß-barrels. We show that UL82 forms a dimer in the crystal as well as in solution. We identify point mutations that disturb the dimerization interface and show that the mutant protein is monomeric in solution and upon expression in human cells. On the basis of the three-dimensional structure, we identify structural homologs of UL82 from other herpesviruses and analyze whether their functions are preserved in UL82. We demonstrate that UL82, despite its structural homology to viral deoxyuridinetriphosphatases (dUTPases), does not possess dUTPase activity. Prompted by the structural homology of UL82 to the ORF10 protein of murine herpesvirus 68 (MHV68), which is known to interact with the RNA export factor ribonucleic acid export 1 (Rae1), we performed coimmunoprecipitations and demonstrated that UL82 indeed interacts with Rae1. This suggests that HCMV UL82 may play a role in mRNA export from the nucleus similar to ORF10 encoded by the gammaherpesviruses MHV68.

Investigating vulnerability of the conserved SARS-CoV-2 spike's heptad repeat 2 as target for fusion inhibitors using chimeric miniproteins

Inhibition of SARS-CoV-2 membrane fusion is a highly desired target to combat COVID-19. The interaction between the spike's heptad repeat (HR) regions 1 (HR1) and 2 (HR2) is a crucial step during the fusion process and these highly conserved HR regions constitute attractive targets for fusion inhibitors. However, the relative importance of each subregion of the long HR1-HR2 interface for viral inhibition remains unclear. Here, we designed, produced, and characterized a series of chimeric miniproteins that mimic two different half subdomains of HR1. The proteins were designed as single polypeptide chains that spontaneously fold into antiparallel trimeric helical bundles aimed at structurally imitate the molecular surface of each HR1 half subregion. All the miniproteins folded stably as helical structures and could bind complementary HR2 peptides with moderate affinity. However, only the miniproteins mimicking the N-terminal HR1 half subdomain, but not those imitating C-terminal one, could inhibit cell infection by SARS-COV-2 real viruses in cell cultures. Most interestingly, the inhibitory activity of the miniproteins correlated with their structural stability, but not with their relative binding affinity for HR2 peptides. These results are highly relevant for designing more focused and active fusion inhibitors targeting the highly conserved HR2 region of the Spike.

Terahertz Time-Domain Spectroscopic (THz-TDS) Insights into Protein Deformation

In this study, we utilized terahertz time-domain spectroscopy (THz-TDS) to study the radiation-induced protein deformation. The absorption coefficient spectra obtained from THz-TDS measurements in the frequency range (0.06–2 THz) was fitted using the Lorentzian model. The absorption coefficient fitting data was used to identify the α-helix and β-structure relative contributions in the protein secondary structure of the kidney tissue of rats irradiated with 10-cGy and 2-Gy X-ray separately or in combination. Our data show that 2-Gy X-irradiation leads to an increase in the β-structure contribution associated with a decrease in the α-helix contribution as indicated by the fitting parameters extracted from fitting the absorption coefficient α(ω) spectra with the Lorentzian function. The results point out that there is a strong correlation between the strength of the hydrogen bonds located between or inside the polypeptide chains of the extended β-sheet and α-helix, respectively, and the absolute value of the absorption coefficient α(ω), the refractive index, and the dielectric constant. The lowest refractive index and dielectric constant are recorded in the 2-Gy-irradiated group followed by the 10-cGy–2 Gy-irradiated group while the least effect was recorded in the 10-cGy-irradiated group. These data provide evidence of the adaptive effect of the 10-cGy X-irradiation delivered 24 h prior to the 2-Gy x-irradiation.

Three-Dimensional Structural Stability and Local Electrostatic Potential at Point Mutations in Spike Protein of SARS-CoV-2 Coronavirus.

The contagiousness of SARS-CoV-2 β-coronavirus is determined by the virus-receptor electrostatic association of its positively charged spike (S) protein with the negatively charged angiotensin converting enzyme-2 (ACE2 receptor) of the epithelial cells. If some mutations occur, the electrostatic potential on the surface of the receptor-binding domain (RBD) could be altered, and the S-ACE2 association could become stronger or weaker. The aim of the current research is to investigate whether point mutations can noticeably alter the electrostatic potential on the RBD and the 3D stability of the S1-subunit of the S-protein. For this purpose, 15 mutants with different hydrophilicity and electric charge (positive, negative, or uncharged) of the substituted and substituting amino acid residues, located on the RBD at the S1-ACE2 interface, are selected, and the 3D structure of the S1-subunit is reconstructed on the base of the crystallographic structure of the S-protein of the wild-type strain and the amino acid sequence of the unfolded polypeptide chain of the mutants. Then, the Gibbs free energy of folding, isoelectric point, and pH-dependent surface electrostatic potential of the S1-subunit are computed using programs for protein electrostatics. The results show alterations in the local electrostatic potential in the vicinity of the mutant amino acid residue, which can influence the S-ACE2 association. This approach allows prediction of the relative infectivity, transmissibility, and contagiousness (at equal social immune status) of new SARS-CoV-2 mutants by reconstruction of the 3D structure of the S1-subunit and calculation of the surface electrostatic potential.

Effects of Germination on the Structure, Functional Properties, and In Vitro Digestibility of a Black Bean (Glycine max (L.) Merr.) Protein Isolate

The utilization of black beans as a protein-rich ingredient presents remarkable prospects in the protein food industry. The objective of this study was to assess the impact of germination treatment on the physicochemical, structural, and functional characteristics of a black bean protein isolate. The findings indicate that germination resulted in an increase in both the total and soluble protein contents of black beans, while SDS-PAGE demonstrated an increase in the proportion of 11S and 7S globulin subunits. After germination, the particle size of the black bean protein isolate decreased in the solution, while the absolute value of the zeta potential increased. The above results show that the stability of the solution was improved. The contents of β-sheet and β-turn gradually decreased, while the content of α-helix increased, and the fluorescence spectrum of the black bean protein isolate showed a red shift phenomenon, indicating that the structure of the protein isolate and its polypeptide chain were prolonged, and the foaming property, emulsification property and in vitro digestibility were significantly improved after germination. Therefore, germination not only improves functional properties, but also nutritional content.

Transient helices with functional roles

Intrinsically disordered regions (IDRs) of proteins contribute to various cellular functions, including signal transduction, gene regulation, and subcellular organization (1). One of the most important aspects of IDRs is their contribution to biomolecular condensate formation within cells. IDRs can undergo multivalent intermolecular interactions that drive phase separation. For the multivalent interactions, IDRs may have preferential interaction sites ('stickers') flanked by inert sequences ('spacers') (1). However, how these interactions occur between conformationally flexible polypeptide chains is not well understood.

Urease from Vigna umbellata seeds: isolation, partial purification, characterization and antifungal activity

Urease (EC 3.5.1.5) hydrolyzes urea to produce ammonia and carbamate. Urease can be synthesized by plants, fungi and bacteria. In agriculture, urease is needed efficiently to play a major role in the urea cycle as source of plant nitrogen in the soil. Rice beans (Vigna umbellata) are leguminous plants from the Fabaceae family that contain high urease activity. This study isolated urease from the seed coat and without the seed coat of rice beans. The urease activity in rice beans without seed coat was higher than that of the activity with seed coat. The amount of ammonia produced with the addition of 1 µL of urease enzyme of rice beans without seed coat was 13 µg which was higher than the amino produced from the seed coat sample (8.8 µg). The concentration of urease enzyme from rice beans was obtained at 7.238 mg/mL. Analyses of gel electrophoresis indicated that urease from rice beans are composed of four polypeptide chains with molecular weights of about 52, 33, 22 and 10 kDa. Then rice beans urease exhibited no antifungal activity against Aspergillus niger, Aspergillus fumigatus, Microsporum canis, Fusarium oxysporum subsp. lini, Trichophyton rubrum, Candida glabrata and Candida albicans.

ABO*A2.08 Subtype Allele Identification and Protein Structure Analysis in Newborns

To study the serological characteristics of ABO*A2.08 subtype and explore its genetic molecular mechanism. ABO blood group identification was performed on proband and her family members by routine serological methods. ABO genotyping and sequence analysis were performed by polymerase chain reaction-sequence specific primer (PCR-SSP), and direct sequencing of PCR products from exons 6 and 7 of ABO gene were directly sequenced and analyzed. The effect of gene mutation in A2.08 subtype on structural stability of GTA protein was investigated by homologous protein conserved analysis, 3D molecular modeling and protein stability prediction. The proband's serological test results showed subtype Ax, and ABO genotyping confirmed that the proband's genotype was ABO*A207/08. Gene sequencing of the proband's father confirmed the characteristic variation of c.539G>C in the 7th exon of ABO gene, leading to the replacement of polypeptide chain p.Arg180Pro (R180P). 3D protein molecular modeling and analysis suggested that the number of hydrogen bonds of local amino acids in the protein structure was changed after the mutation, and protein stability prediction showed that the mutation had a great influence on the protein structure stability. The mutation of the 7th exon c.539G>C of ABO gene leads to the substitution of polypeptide chain amino acid, which affects the structural stability of GTA protein and leads to the change of enzyme activity, resulting in the A2.08 phenotype. The mutated gene can be stably inherited.

Amino Acid Polymerization on Silica Surfaces.

The polymerization of unactivated amino acids (AAs) is an important topic because of its applications in various fields including industrial medicinal chemistry and prebiotic chemistry. Silica as a promoter for this reaction, is of great interest owing to its large abundance and low cost. The amide/peptide bond synthesis on silica has been largely demonstrated but suffers from a lack of knowledge regarding its reaction mechanism, the key parameters, and surface features that influence AA adsorption and reactivity, the selectivity of the reaction product, the role of water in the reaction, etc. The present review addresses these problems by summarizing experimental and modeling results from the literature and attempts to rationalize some apparent divergences in published results. After briefly presenting the main types of silica surface sites and other relevant macroscopic features, we discuss the different deposition procedures of AAs, whose importance is often neglected. We address the possible AA adsorption mechanisms including covalent grafting and H-bonding and show that they are highly dependent on silanol types and density. We then consider how the adsorption mechanisms determine the occurrence and outcome of AA condensation (formation of cyclic dimers or of long linear chains), and outline some recent results that suggest significant polymerization selectivity in systems containing several AAs, as well as the formation of specific elements of secondary structure in the growing polypeptide chains.