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Journal articles on the topic 'Protein chemistry'

To see the other types of publications on this topic, follow the link: Protein chemistry.

Author: Grafiati

Published: 4 June 2021

Last updated: 7 September 2023

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1

Bera, Smritilekha, and Dhananjoy Mondal. "Click-Chemistry-Assisted Alteration of Glycosaminoglycans for Biological Applications." SynOpen 07, no. 02 (June 2023): 277–89. http://dx.doi.org/10.1055/s-0040-1720072.

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AbstractThis short review describes the assistance of click chemistry in the chemical modification of glycosaminoglycans. Through an alkyne-azide 1,3-dipolar cycloaddition reaction, the chemically and physiologically stable triazole unit connects glycosaminoglycans with other labelled or attached functionalities. The synthesized glycosaminoglycan (GAG) conjugates act as drug carriers, forming hydrogels or nanohydrogels for localized drug delivery or injectable GAGs and so on. These are used in research on antithrombotic agents, protein binding, and hepatocyte growth factors, as well as in mechanistic studies of glycosaminoglycans biosynthesis and wound healing.1 Introduction2 Synthetic Modification of GAGS3 Click Chemistry4 Modification of GAGS Applying Click Chemistry5 Conclusions6 Abbreviations

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2

GUO, ATHENA, and XIAOYANG ZHU. "SURFACE CHEMISTRY FOR PROTEIN MICROARRAYS." International Journal of Nanoscience 06, no. 02 (April 2007): 109–16. http://dx.doi.org/10.1142/s0219581x07004341.

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Protein microarray or protein chip is an important tool in proteomics. However, duplicating the success of the DNA chip for the protein chip has been difficult. This account discusses a key issue in protein microarray development, i.e., surface chemistry. Ideally, the surface chemistry for protein microarray fabrication should satisfy the following criteria: the surface resists nonspecific adsorption; functional groups for the facile immobilization of protein molecules of interest are readily available; bonding between a protein molecule and a solid surface is balanced to provide sufficient stability but minimal disturbance on the delicate three-dimensional structure of the protein; linking chemistry allows the control of protein orientation; the local chemical environment favors the immobilized protein molecules to retain their native conformation; and finally, the specificity of linking chemistry is so high that no pre-purification of proteins is required. Strategies to achieve such an ideal situation are discussed, with successful examples from our laboratories illustrated. Finally, the need of surface technology for membrane protein microarray fabrication is addressed.

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3

KANAYA, Shigenori. ""Latest protein chemistry"." Journal of Synthetic Organic Chemistry, Japan 49, no. 8 (1991): 775–79. http://dx.doi.org/10.5059/yukigoseikyokaishi.49.775.

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4

Scheraga, Harold A. "My 65 years in protein chemistry." Quarterly Reviews of Biophysics 48, no. 2 (April 8, 2015): 117–77. http://dx.doi.org/10.1017/s0033583514000134.

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AbstractThis is a tour of a physical chemist through 65 years of protein chemistry from the time when emphasis was placed on the determination of the size and shape of the protein molecule as a colloidal particle, with an early breakthrough by James Sumner, followed by Linus Pauling and Fred Sanger, that a protein was a real molecule, albeit a macromolecule. It deals with the recognition of the nature and importance of hydrogen bonds and hydrophobic interactions in determining the structure, properties, and biological function of proteins until the present acquisition of an understanding of the structure, thermodynamics, and folding pathways from a linear array of amino acids to a biological entity. Along the way, with a combination of experiment and theoretical interpretation, a mechanism was elucidated for the thrombin-induced conversion of fibrinogen to a fibrin blood clot and for the oxidative-folding pathways of ribonuclease A. Before the atomic structure of a protein molecule was determined by x-ray diffraction or nuclear magnetic resonance spectroscopy, experimental studies of the fundamental interactions underlying protein structure led to several distance constraints which motivated the theoretical approach to determine protein structure, and culminated in the Empirical Conformational Energy Program for Peptides (ECEPP), an all-atom force field, with which the structures of fibrous collagen-like proteins and the 46-residue globular staphylococcal protein A were determined. To undertake the study of larger globular proteins, a physics-based coarse-grained UNited-RESidue (UNRES) force field was developed, and applied to the protein-folding problem in terms of structure, thermodynamics, dynamics, and folding pathways. Initially, single-chain and, ultimately, multiple-chain proteins were examined, and the methodology was extended to protein–protein interactions and to nucleic acids and to protein–nucleic acid interactions. The ultimate results led to an understanding of a variety of biological processes underlying natural and disease phenomena.

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5

Shoichet, Brian K., and Irwin D. Kuntz. "Matching chemistry and shape in molecular docking." "Protein Engineering, Design and Selection" 6, no. 7 (1993): 723–32. http://dx.doi.org/10.1093/protein/6.7.723.

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6

Metanis, Norman, Reem Mousa, and Post Reddy. "Chemical Protein Synthesis through Selenocysteine Chemistry." Synlett 28, no. 12 (March 21, 2017): 1389–93. http://dx.doi.org/10.1055/s-0036-1588762.

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Methods for the preparation of small-to-medium-sized proteins by chemical protein synthesis have matured in recent years and proven valuable for protein science. Thanks to the many recent discoveries and developments in the field, proteins up to 300 amino acids can now be prepared in the lab in a matter of days. This technology gives the scientists the flexibility to substitute any atom in the protein sequence; hence synthesis is not constrained to the 20 canonical amino acids. In this Synpacts article we briefly highlight the recent studies on selenocysteine chemistry in the field of chemical protein synthesis.1 Introduction2 Selenocysteine in Nature and in Folding Studies3 Selenocysteine in Protein Synthesis4 Selenocysteine in Natural Selenoproteins5 Outlook

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7

Uhlén, Mathias, and Per-Åke Nygren. "Combinatorial Protein Chemistry- New Proteins With Selective Binding." Biochemical Society Transactions 28, no. 5 (October 1, 2000): A125. http://dx.doi.org/10.1042/bst028a125b.

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8

Bayer, Peter, Anja Matena, and Christine Beuck. "NMR Spectroscopy of supramolecular chemistry on protein surfaces." Beilstein Journal of Organic Chemistry 16 (October 9, 2020): 2505–22. http://dx.doi.org/10.3762/bjoc.16.203.

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As one of the few analytical methods that offer atomic resolution, NMR spectroscopy is a valuable tool to study the interaction of proteins with their interaction partners, both biomolecules and synthetic ligands. In recent years, the focus in chemistry has kept expanding from targeting small binding pockets in proteins to recognizing patches on protein surfaces, mostly via supramolecular chemistry, with the goal to modulate protein–protein interactions. Here we present NMR methods that have been applied to characterize these molecular interactions and discuss the challenges of this endeavor.

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9

Wood, EJ. "Structure in protein chemistry." Biochemical Education 24, no. 1 (January 1996): 68–69. http://dx.doi.org/10.1016/s0307-4412(96)80028-8.

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10

Ashman, Keith, and Matthias Mann. "Cordon bleu protein chemistry." Trends in Biochemical Sciences 20, no. 12 (December 1995): 528–29. http://dx.doi.org/10.1016/s0968-0004(00)89124-0.

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11

Soutar, Anne K. "Advances in protein chemistry." Trends in Endocrinology & Metabolism 6, no. 5 (July 1995): 184–85. http://dx.doi.org/10.1016/1043-2760(95)90049-7.

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12

Dräger, Gerald. "Peptide and Protein Chemistry." Nachrichten aus der Chemie 52, no. 6 (June 2004): 719. http://dx.doi.org/10.1002/nadc.20040520635.

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13

Tesser, G. I., and P. J. Boon. "Semisynthesis in protein chemistry." Recueil des Travaux Chimiques des Pays-Bas 99, no. 10 (September 2, 2010): 289–300. http://dx.doi.org/10.1002/recl.19800991001.

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14

Reddington, Samuel, Peter Watson, Pierre Rizkallah, Eric Tippmann, and D. Dafydd Jones. "Genetically encoding phenyl azide chemistry: new uses and ideas for classical biochemistry." Biochemical Society Transactions 41, no. 5 (September 23, 2013): 1177–82. http://dx.doi.org/10.1042/bst20130094.

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Introducing new physicochemical properties into proteins through genetically encoded Uaa (unnatural amino acid) incorporation can lead to the generation of proteins with novel properties not normally accessible with the 20 natural amino acids. Phenyl azide chemistry represents one such useful addition to the protein repertoire. Classically used in biochemistry as a non-specific photochemical protein cross-linker, genetically encoding phenyl azide chemistry at selected residues provides more powerful routes to post-translationally modify protein function in situ. The two main routes are modulation by light (optogenetics) and site-specific bio-orthogonal modification (bioconjugation) via Click chemistry. In the present article, we discuss both approaches and their influence on protein function.

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15

Matyshevska, O. P., M. V. Grigorieva, V. M. Danilova, and S. V. Komisarenko. "Ubiquitin and its role in proteolisis: the 2004 Nobel prize in chemistry." Ukrainian Biochemical Journal 94, no. 5 (December 8, 2022): 84–96. http://dx.doi.org/10.15407/ubj94.05.084.

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In the early 1980-s, Aaron Ciechanover, Avram Hershko, and Irwin Rose discovered one of the most important cyclic cellular processes – a regulated ATP-dependent protein degradation, for which they were awarded the 2004 Nobel Prize in Chemistry. These scientists proved the existence of a non-lysosomal proteolysis pathway and completely changed the perception of intracellular protein degradation mechanisms. They demonstrated pre-labelling of a doomed protein in a cell with a biochemical marker called ubiquitin. Polyubiquitylation of a protein as a signal for its proteolysis was a new mechanism discovered as a result of collaborative efforts of three scientists on isolation of enzymes involved in this sequential process, clarification of the biochemical stages, and substantiating the energy dependence mechanism. The article contains biographical data of the Nobel laureates, the methods applied, and the history of the research resulted in the discovery of the phenomenon of proteasomal degradation of ubiquitin-mediated proteins. Keywords: PROTAC, regulated protein degradation, ubiquitin, І. Rose, А. Ciechanover, А. Hershko

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16

Stollar, Elliott J., and David P. Smith. "Uncovering protein structure." Essays in Biochemistry 64, no. 4 (September 25, 2020): 649–80. http://dx.doi.org/10.1042/ebc20190042.

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Abstract Structural biology is the study of the molecular arrangement and dynamics of biological macromolecules, particularly proteins. The resulting structures are then used to help explain how proteins function. This article gives the reader an insight into protein structure and the underlying chemistry and physics that is used to uncover protein structure. We start with the chemistry of amino acids and how they interact within, and between proteins, we also explore the four levels of protein structure and how proteins fold into discrete domains. We consider the thermodynamics of protein folding and why proteins misfold. We look at protein dynamics and how proteins can take on a range of conformations and states. In the second part of this review, we describe the variety of methods biochemists use to uncover the structure and properties of proteins that were described in the first part. Protein structural biology is a relatively new and exciting field that promises to provide atomic-level detail to more and more of the molecules that are fundamental to life processes.

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17

Westerlund, Kristina, Sean D. Moran, Heidi K. Privett, Sam Hay, Jüri Jarvet, Brian R. Gibney, and Cecilia Tommos. "Making a single-chain four-helix bundle for redox chemistry studies." Protein Engineering, Design and Selection 21, no. 11 (August 28, 2008): 645–52. http://dx.doi.org/10.1093/protein/gzn043.

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18

Sato and Nakamura. "Protein Chemical Labeling Using Biomimetic Radical Chemistry." Molecules 24, no. 21 (November 3, 2019): 3980. http://dx.doi.org/10.3390/molecules24213980.

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Chemical labeling of proteins with synthetic low-molecular-weight probes is an important technique in chemical biology. To achieve this, it is necessary to use chemical reactions that proceed rapidly under physiological conditions (i.e., aqueous solvent, pH, low concentration, and low temperature) so that protein denaturation does not occur. The radical reaction satisfies such demands of protein labeling, and protein labeling using the biomimetic radical reaction has recently attracted attention. The biomimetic radical reaction enables selective labeling of the C-terminus, tyrosine, and tryptophan, which is difficult to achieve with conventional electrophilic protein labeling. In addition, as the radical reaction proceeds selectively in close proximity to the catalyst, it can be applied to the analysis of protein–protein interactions. In this review, recent trends in protein labeling using biomimetic radical reactions are discussed.

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19

Sanghamitra, Nusrat J. M., and Takafumi Ueno. "Expanding coordination chemistry from protein to protein assembly." Chem. Commun. 49, no. 39 (2013): 4114–26. http://dx.doi.org/10.1039/c2cc36935d.

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20

Vogel, G. "PROTEIN CHEMISTRY: A Two-Piece Protein Assembles Itself." Science 281, no. 5378 (August 7, 1998): 763a—764. http://dx.doi.org/10.1126/science.281.5378.763a.

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21

Reddy, Neelesh C., Mohan Kumar, Rajib Molla, and Vishal Rai. "Chemical methods for modification of proteins." Organic & Biomolecular Chemistry 18, no. 25 (2020): 4669–91. http://dx.doi.org/10.1039/d0ob00857e.

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The field of protein bioconjugation draws attention from stakeholders in chemistry, biology, and medicine. This review provides an overview of the present status, challenges, and opportunities for organic chemists.

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22

Besley, Nicholas A. "Computing protein infrared spectroscopy with quantum chemistry." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 365, no. 1861 (September 13, 2007): 2799–812. http://dx.doi.org/10.1098/rsta.2007.0018.

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Quantum chemistry is a field of science that has undergone unprecedented advances in the last 50 years. From the pioneering work of Boys in the 1950s, quantum chemistry has evolved from being regarded as a specialized and esoteric discipline to a widely used tool that underpins much of the current research in chemistry today. This achievement was recognized with the award of the 1998 Nobel Prize in Chemistry to John Pople and Walter Kohn. As the new millennium unfolds, quantum chemistry stands at the forefront of an exciting new era. Quantitative calculations on systems of the magnitude of proteins are becoming a realistic possibility, an achievement that would have been unimaginable to the early pioneers of quantum chemistry. In this article we will describe ongoing work towards this goal, focusing on the calculation of protein infrared amide bands directly with quantum chemical methods.

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23

Shortle, David. "Mutational studies of protein structures and their stabilities." Quarterly Reviews of Biophysics 25, no. 2 (May 1992): 205–50. http://dx.doi.org/10.1017/s0033583500004674.

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The fundamental relationship between structure and function has served to guide investigations into the workings of living systems at all levels - from the whole organism to individual cells on down to individual molecules. When X-ray crystallography began to reveal the three-dimensional structures of proteins like myoglobin, lysozyme and RNase A, protein chemists were well prepared to draw inferences about functional mechanisms from the precise positioning of amino acid residues they could see. The close proximity between an amino acid side chain and a chemical group on a bound ligand strongly suggests a functional role for that side chain in binding affinity and specificity. Likewise, the nearly universal finding of large clusters of hydrophobic side chains buried in the core of proteins strongly supports a major functional role of hydrophobic interactions in protein folding and stability. Even though eminently plausible hypotheses like these, grounded in the most fundamental principles of chemistry and the logic of structure–function relationships, become widely accepted and make their way into textbooks, protein chemists have felt compelled to search for ways to test them and put them on a more quantitative basis.

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24

Lavine, M. "CHEMISTRY: Shaped by a Protein." Science 316, no. 5826 (May 11, 2007): 801a. http://dx.doi.org/10.1126/science.316.5826.801a.

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25

Service, Robert F. "Protein evolution earns chemistry Nobel." Science 362, no. 6411 (October 11, 2018): 142. http://dx.doi.org/10.1126/science.362.6411.142.

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26

Whitaker, Tim. "Protein experts scoop chemistry prize." Physics World 15, no. 11 (November 2002): 9. http://dx.doi.org/10.1088/2058-7058/15/11/9.

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27

Sugai, Shintaro, and Masamichi Ikeguchi. "Physical Chemistry of Protein Folding." Kobunshi 40, no. 9 (1991): 624–27. http://dx.doi.org/10.1295/kobunshi.40.624.

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28

Fraenkel‐Conrat, Heinz. "Early Days of Protein Chemistry." FASEB Journal 8, no. 6 (April 1994): 452–53. http://dx.doi.org/10.1096/fasebj.8.6.8168696.

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29

Fahrenkamp-Uppenbrink, J. "PROTEIN CHEMISTRY: An Easy Switch." Science 309, no. 5732 (July 8, 2005): 223a. http://dx.doi.org/10.1126/science.309.5732.223a.

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30

Wisemann, Alan. "Practical Protein Chemistry-A Handbook." Analytica Chimica Acta 186 (1986): 346–47. http://dx.doi.org/10.1016/s0003-2670(00)81819-x.

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31

Walker, JohnM. "Techniques in protein chemistry II." FEBS Letters 297, no. 3 (February 10, 1992): 307. http://dx.doi.org/10.1016/0014-5793(92)80563-v.

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32

Landon, M. "Practical protein chemistry - a handbook." FEBS Letters 210, no. 1 (January 1, 1987): 107–8. http://dx.doi.org/10.1016/0014-5793(87)81310-8.

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33

Cooper, EdwardH. "Practical protein chemistry — A handbook." TrAC Trends in Analytical Chemistry 6, no. 2 (February 1987): 54. http://dx.doi.org/10.1016/0165-9936(87)87013-9.

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34

Holliday, Gemma L., Daniel E. Almonacid, John B. O. Mitchell, and Janet M. Thornton. "The Chemistry of Protein Catalysis." Journal of Molecular Biology 372, no. 5 (October 2007): 1261–77. http://dx.doi.org/10.1016/j.jmb.2007.07.034.

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35

S.J.P. "Techniques in protein chemistry II." Trends in Biochemical Sciences 17, no. 1 (January 1992): 47. http://dx.doi.org/10.1016/0968-0004(92)90430-h.

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36

Marshak, Daniel R., and Gene A. Homandberg. "TECHNIQUES IN PROTEIN CHEMISTRY VII." Shock 6, no. 6 (December 1996): 453. http://dx.doi.org/10.1097/00024382-199612000-00012.

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37

Danson, M. J. "Practical protein chemistry. A handbook." Endeavour 11, no. 1 (January 1987): 53. http://dx.doi.org/10.1016/0160-9327(87)90179-7.

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38

Light, Albert. "Practical protein chemistry—A handbook." Analytical Biochemistry 161, no. 1 (February 1987): 226–27. http://dx.doi.org/10.1016/0003-2697(87)90676-2.

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39

Bairagya, Hridoy R., and Bishnu P. Mukhopadhyay. "Protein folding: challenge to chemistry." Journal of Biomolecular Structure and Dynamics 31, no. 9 (September 2013): 993–94. http://dx.doi.org/10.1080/07391102.2012.748537.

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40

Kauffman, Stuart. "Protein mediated networks. Random chemistry." Berichte der Bunsengesellschaft für physikalische Chemie 98, no. 9 (September 1994): 1142–47. http://dx.doi.org/10.1002/bbpc.19940980915.

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41

Dong, Shouliang, Luis Moroder, and Nediljko Budisa. "Protein Iodination by Click Chemistry." ChemBioChem 10, no. 7 (May 4, 2009): 1149–51. http://dx.doi.org/10.1002/cbic.200800816.

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42

Arkus, Kiani A. J., and Joseph M. Jez. "An integrated protein chemistry laboratory." Biochemistry and Molecular Biology Education 36, no. 2 (2008): 125–28. http://dx.doi.org/10.1002/bmb.20156.

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43

Cringoli, Maria Cristina, and Silvia Marchesan. "Cysteine Redox Chemistry in Peptide Self-Assembly to Modulate Hydrogelation." Molecules 28, no. 13 (June 24, 2023): 4970. http://dx.doi.org/10.3390/molecules28134970.

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Cysteine redox chemistry is widely used in nature to direct protein assembly, and in recent years it has inspired chemists to design self-assembling peptides too. In this concise review, we describe the progress in the field focusing on the recent advancements that make use of Cys thiol–disulfide redox chemistry to modulate hydrogelation of various peptide classes.

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44

Dallemagne, Patrick, Christophe Rochais, Pascal Marchand, and Thierry Besson. "26th Annual GP2A Medicinal Chemistry Conference & 32nd Journées Franco-Belges de Pharmacochimie." Pharmaceuticals 12, no. 2 (May 16, 2019): 73. http://dx.doi.org/10.3390/ph12020073.

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As a joint meeting, the 26th Medicinal Chemistry Conference of GP2A and 32nd Journées Franco-Belges de Pharmacochimie took place between 13th and 15th June at Asnelles sur Mer (Normandie, France), providing a unique opportunity for a wide group of European medicinal chemists to engage. Topics included chemical tools for medicinal chemistry, protein-protein interactions, epigenetics, natural product-inspired molecules, computer-aided drug design, and new strategies for the design and development of drugs. Abstracts of invited lectures, proffered young researcher communications, flash communications and posters presented during the meeting are collected in this report.

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45

Kajal and Anu Radha Pathania. "Chemistry behind Serum Albumin: A Review." E3S Web of Conferences 309 (2021): 01086. http://dx.doi.org/10.1051/e3sconf/202130901086.

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This review informs about the chemical composition of plasma proteins majorly albumin and globulin. Blood proteins, also called plasma proteins, are found in blood plasma. While, serum proteins are present in the human body in very high quantities for other proteins. Hundreds of proteins are dissolved in the plasma but only two major protein groups are present i.e. Albumin and Globulin. Albumin is a very important component (55% of blood proteins) and it is made by the liver. There is an immediate correlation between albumin turnover and body size. Globulin is formed from different proteins called alpha, beta, and gamma types (38% of blood proteins) but a number of the globulins are mainly made by the liver, while others are made by the immune system. The average serum protein level existing in the human body is 6 to 8g/dl but 3.5 to 5.0g/dl is making up only albumin and globulin makes up 2/3gl. Different aspects of the proteins are discussed below.

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46

Wierenga, Rik K., and Dagmar Ringe. "The EMBO biocatalysis conference “The biochemistry and chemistry of biocatalysis: from understanding to design”." Protein Engineering, Design and Selection 30, no. 3 (March 2017): 141. http://dx.doi.org/10.1093/protein/gzx020.

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47

Otaka, Akira, and Akira Shigenaga. "Protein Synthetic Chemistry Inspired by Intein-mediated Protein Splicing." Journal of Synthetic Organic Chemistry, Japan 76, no. 1 (2018): 45–54. http://dx.doi.org/10.5059/yukigoseikyokaishi.76.45.

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48

Lin, Zhanglin, Qiao Lin, Jiahui Li, Marco Pistolozzi, Lei Zhao, Xiaofeng Yang, and Yanrui Ye. "Spy chemistry‐enabled protein directional immobilization and protein purification." Biotechnology and Bioengineering 117, no. 10 (June 30, 2020): 2923–32. http://dx.doi.org/10.1002/bit.27460.

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49

Lin, Hening, and Virginia W. Cornish. "In Vivo Protein-Protein Interaction Assays: Beyond Proteins." Angewandte Chemie International Edition 40, no. 5 (March 2, 2001): 871–75. http://dx.doi.org/10.1002/1521-3773(20010302)40:5<871::aid-anie871>3.0.co;2-s.

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50

Jiang, Luyong, Michel Favre, Kerstin Moehle, and John A. Robinson. "ChemInform Abstract: The Supramolecular Chemistry of Proteins-Protein Epitope Mimetics Prepared Using Combinatorial Biomimetic Chemistry." ChemInform 32, no. 17 (April 24, 2001): no. http://dx.doi.org/10.1002/chin.200117264.

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