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1.
Revisiting sORFs: overcoming challenges to identify and characterize functional microproteins.
Schlesinger, D, Elsässer, SJ
The FEBS journal. 2022;(1):53-74
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Abstract
Short ORFs (sORFs), that is, occurrences of a start and stop codon within 100 codons or less, can be found in organisms of all domains of life, outnumbering annotated protein-coding ORFs by orders of magnitude. Even though functional proteins smaller than 100 amino acids are known, the coding potential of sORFs has often been overlooked, as it is not trivial to predict and test for functionality within the large number of sORFs. Recent advances in ribosome profiling and mass spectrometry approaches, together with refined bioinformatic predictions, have enabled a huge leap forward in this field and identified thousands of likely coding sORFs. A relatively low number of small proteins or microproteins produced from these sORFs have been characterized so far on the molecular, structural, and/or mechanistic level. These however display versatile and, in some cases, essential cellular functions, allowing for the exciting possibility that many more, previously unknown small proteins might be encoded in the genome, waiting to be discovered. This review will give an overview of the steadily growing microprotein field, focusing on eukaryotic small proteins. We will discuss emerging themes in the molecular action of microproteins, as well as advances and challenges in microprotein identification and characterization.
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2.
Role of Ionic Strength in the Formation of Stable Supramolecular Nanoparticle-Protein Conjugates for Biosensing.
Brancolini, G, Rotello, VM, Corni, S
International journal of molecular sciences. 2022;(4)
Abstract
Monolayer-protected gold nanoparticles (AuNPs) exhibit distinct physical and chemical properties depending on the nature of the ligand chemistry. A commonly employed NP monolayer comprises hydrophobic molecules linked to a shell of PEG and terminated with functional end group, which can be charged or neutral. Different layers of the ligand shell can also interact in different manners with proteins, expanding the range of possible applications of these inorganic nanoparticles. AuNP-fluorescent Green Fluorescent Protein (GFP) conjugates are gaining increasing attention in sensing applications. Experimentally, their stability is observed to be maintained at low ionic strength conditions, but not at physiologically relevant conditions of higher ionic strength, limiting their applications in the field of biosensors. While a significant amount of fundamental work has been done to quantify electrostatic interactions of colloidal nanoparticle at the nanoscale, a theoretical description of the ion distribution around AuNPs still remains relatively unexplored. We perform extensive atomistic simulations of two oppositely charged monolayer-protected AuNPs interacting with fluorescent supercharged GFPs co-engineered to have complementary charges. These simulations were run at different ionic strengths to disclose the role of the ionic environment on AuNP-GFP binding. The results highlight the capability of both AuNPs to intercalate ions and water molecules within the gold-sulfur inner shell and the different tendency of ligands to bend inward allowing the protein to bind not only with the terminal ligands but also the hydrophobic alkyl chains. Different binding stability is observed in the two investigated cases as a function of the ligand chemistry.
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3.
Optical Configuration Effect on the Structure and Reactivity of Diastereomers Revealed by Spin Effects and Molecular Dynamics Calculations.
Ageeva, AA, Doktorov, AB, Selyutina, OY, Magin, IM, Ilyina, MG, Borisevich, SS, Rubtsov, RY, Khursan, SL, Stepanov, AA, Vasilevsky, SF, et al
International journal of molecular sciences. 2021;(1)
Abstract
The peculiarities of spin effects in photoinduced electron transfer (ET) in diastereomers of donor-acceptor dyads are considered in order to study the influence of chirality on reactivity. Thus, the spin selectivity-the difference between the enhancement coefficients of chemically induced dynamic nuclear polarization (CIDNP)-of the dyad's diastereomers reflects the difference in the spin density distribution in its paramagnetic precursors that appears upon UV irradiation. In addition, the CIDNP coefficient itself has demonstrated a high sensitivity to the change of chiral centers: when one center is changed, the hyperpolarization of all polarized nuclei of the molecule is affected. The article analyzes the experimental values of spin selectivity based on CIDNP calculations and molecular dynamic modeling data in order to reveal the effect of optical configuration on the structure and reactivity of diastereomers. In this way, we succeeded in tracing the differences in dyads with L- and D-tryptophan as an electron donor. Since the replacement of L-amino acid with D-analog in specific proteins is believed to be the cause of Alzheimer's and Parkinson's diseases, spin effects and molecular dynamic simulation in model dyads can be a useful tool for investigating the nature of this phenomenon.
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4.
Water molecules at protein-drug interfaces: computational prediction and analysis methods.
Samways, ML, Taylor, RD, Bruce Macdonald, HE, Essex, JW
Chemical Society reviews. 2021;(16):9104-9120
Abstract
The fundamental importance of water molecules at drug-protein interfaces is now widely recognised and a significant feature in structure-based drug design. Experimental methods for analysing the role of water in drug binding have many challenges, including the accurate location of bound water molecules in crystal structures, and problems in resolving specific water contributions to binding thermodynamics. Computational analyses of binding site water molecules provide an alternative, and in principle complete, structural and thermodynamic picture, and their use is now commonplace in the pharmaceutical industry. In this review, we describe the computational methodologies that are available and discuss their strengths and weaknesses. Additionally, we provide a critical analysis of the experimental data used to validate the methods, regarding the type and quality of experimental structural data. We also discuss some of the fundamental difficulties of each method and suggest directions for future study.
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Interchangeable utilization of metals: New perspectives on the impacts of metal ions employed in ancient and extant biomolecules.
Smethurst, DGJ, Shcherbik, N
The Journal of biological chemistry. 2021;(6):101374
Abstract
Metal ions provide considerable functionality across biological systems, and their utilization within biomolecules has adapted through changes in the chemical environment to maintain the activity they facilitate. While ancient earth's atmosphere was rich in iron and manganese and low in oxygen, periods of atmospheric oxygenation significantly altered the availability of certain metal ions, resulting in ion replacement within biomolecules. This adaptation mechanism has given rise to the phenomenon of metal cofactor interchangeability, whereby contemporary proteins and nucleic acids interact with multiple metal ions interchangeably, with different coordinated metals influencing biological activity, stability, and toxic potential. The ability of extant organisms to adapt to fluctuating metal availability remains relevant in a number of crucial biomolecules, including the superoxide dismutases of the antioxidant defense systems and ribonucleotide reductases. These well-studied and ancient enzymes illustrate the potential for metal interchangeability and adaptive utilization. More recently, the ribosome has also been demonstrated to exhibit interchangeable interactions with metal ions with impacts on function, stability, and stress adaptation. Using these and other examples, here we review the biological significance of interchangeable metal ions from a new angle that combines both biochemical and evolutionary viewpoints. The geochemical pressures and chemical properties that underlie biological metal utilization are discussed in the context of their impact on modern disease states and treatments.
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Cyclodextrins based delivery systems for macro biomolecules.
Liu, J, Ding, X, Fu, Y, Xiang, C, Yuan, Y, Zhang, Y, Yu, P
European journal of medicinal chemistry. 2021;:113105
Abstract
Macro biomolecules are of vital importance in regulating the biofunctions in organisms, in which proteins (including peptides when mentioned below) and nucleic acids (NAs) are the most important. Therefore, these proteins and NAs can be applied as "drugs" to regulate the biofunctions from abnormal to normal. Either for proteins and NAs, the most challenging thing is to avoid the biodegradation or physicochemical degradation before they reach the targeted location, and then functions as complete functional structures. Hence, appropriate delivery systems are very important which can protect them from these degradations. Cyclodextrins (CDs) based delivery systems achieved mega successes due to their outstanding pharmaceutical properties and there have been several reviews on CDs based small molecule drug delivery systems recently. But for biomolecules, which are getting more and more important for modern therapies, however, there are very few reviews to systematically summarize and analyze the CDs-based macro biomolecules delivery systems, especially for proteins. In this review, there were some of the notable examples were summarized for the macro biomolecules (proteins and NAs) delivery based on CDs. For proteins, this review included insulin, lysozyme, bovine serum albumin (BSA), green fluorescent protein (GFP) and IgG's, etc. deliveries in slow release, stimulating responsive release or targeting release manners. For NAs, this review summarized cationic CD-polymers and CD-cluster monomers as NAs carriers, notably, including the multicomponents targeting CD-based carriers and the virus-like RNA assembly method siRNA carriers.
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7.
Functional biomedical materials derived from proteins in the acquired salivary pellicle.
Zhang, F, Cheng, Z, Ding, C, Li, J
Journal of materials chemistry. B. 2021;(33):6507-6520
Abstract
In the oral environment, the acquired salivary pellicle (ASP) on the tooth surface comprises proteins, glycoproteins, carbohydrates, and lipids. The ASP can specifically and rapidly adsorb on the enamel surface to provide effective lubrication, protection, hydration, and remineralisation, as well as be recognised by various bacteria to form a microbial biofilm (plaque). The involved proteins, particularly various phosphoproteins such as statherins, histatins, and proline-rich proteins, are vital to their specific functions. This review first describes the relationship between the biological functions of these proteins and their structures. Subsequently, recent advances in functional biomedical materials derived from these proteins are reviewed in terms of dental/bone therapeutic materials, antibacterial materials, tissue engineering materials, and coatings for medical devices. Finally, perspectives and challenges regarding the rational design and biomedical applications of ASP-derived materials are discussed.
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8.
PredNTS: Improved and Robust Prediction of Nitrotyrosine Sites by Integrating Multiple Sequence Features.
Nilamyani, AN, Auliah, FN, Moni, MA, Shoombuatong, W, Hasan, MM, Kurata, H
International journal of molecular sciences. 2021;(5)
Abstract
Nitrotyrosine, which is generated by numerous reactive nitrogen species, is a type of protein post-translational modification. Identification of site-specific nitration modification on tyrosine is a prerequisite to understanding the molecular function of nitrated proteins. Thanks to the progress of machine learning, computational prediction can play a vital role before the biological experimentation. Herein, we developed a computational predictor PredNTS by integrating multiple sequence features including K-mer, composition of k-spaced amino acid pairs (CKSAAP), AAindex, and binary encoding schemes. The important features were selected by the recursive feature elimination approach using a random forest classifier. Finally, we linearly combined the successive random forest (RF) probability scores generated by the different, single encoding-employing RF models. The resultant PredNTS predictor achieved an area under a curve (AUC) of 0.910 using five-fold cross validation. It outperformed the existing predictors on a comprehensive and independent dataset. Furthermore, we investigated several machine learning algorithms to demonstrate the superiority of the employed RF algorithm. The PredNTS is a useful computational resource for the prediction of nitrotyrosine sites. The web-application with the curated datasets of the PredNTS is publicly available.
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9.
Computational models in the service of X-ray and cryo-electron microscopy structure determination.
Kryshtafovych, A, Moult, J, Albrecht, R, Chang, GA, Chao, K, Fraser, A, Greenfield, J, Hartmann, MD, Herzberg, O, Josts, I, et al
Proteins. 2021;(12):1633-1646
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Abstract
Critical assessment of structure prediction (CASP) conducts community experiments to determine the state of the art in computing protein structure from amino acid sequence. The process relies on the experimental community providing information about not yet public or about to be solved structures, for use as targets. For some targets, the experimental structure is not solved in time for use in CASP. Calculated structure accuracy improved dramatically in this round, implying that models should now be much more useful for resolving many sorts of experimental difficulties. To test this, selected models for seven unsolved targets were provided to the experimental groups. These models were from the AlphaFold2 group, who overall submitted the most accurate predictions in CASP14. Four targets were solved with the aid of the models, and, additionally, the structure of an already solved target was improved. An a posteriori analysis showed that, in some cases, models from other groups would also be effective. This paper provides accounts of the successful application of models to structure determination, including molecular replacement for X-ray crystallography, backbone tracing and sequence positioning in a cryo-electron microscopy structure, and correction of local features. The results suggest that, in future, there will be greatly increased synergy between computational and experimental approaches to structure determination.
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10.
A Rosetta-based protein design protocol converging to natural sequences.
Sormani, G, Harteveld, Z, Rosset, S, Correia, B, Laio, A
The Journal of chemical physics. 2021;(7):074114
Abstract
Computational protein design has emerged as a powerful tool capable of identifying sequences compatible with pre-defined protein structures. The sequence design protocols, implemented in the Rosetta suite, have become widely used in the protein engineering community. To understand the strengths and limitations of the Rosetta design framework, we tested several design protocols on two distinct folds (SH3-1 and Ubiquitin). The sequence optimization, when started from native structures and natural sequences or polyvaline sequences, converges to sequences that are not recognized as belonging to the fold family of the target protein by standard bioinformatic tools, such as BLAST and Hmmer. The sequences generated from both starting conditions (native and polyvaline) are instead very similar to each other and recognized by Hmmer as belonging to the same "family." This demonstrates the capability of Rosetta to converge to similar sequences, even when sampling from distinct starting conditions, but, on the other hand, shows intrinsic inaccuracy of the scoring function that drifts toward sequences that lack identifiable natural sequence signatures. To address this problem, we developed a protocol embedding Rosetta Design simulations in a genetic algorithm, in which the sequence search is biased to converge to sequences that exist in nature. This protocol allows us to obtain sequences that have recognizable natural sequence signatures and, experimentally, the designed proteins are biochemically well behaved and thermodynamically stable.