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  1. AU="Kilgore, Henry R"
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  1. Article ; Online: Learning the chemical grammar of biomolecular condensates.

    Kilgore, Henry R / Young, Richard A

    Nature chemical biology

    2022  Volume 18, Issue 12, Page(s) 1298–1306

    Abstract: Biomolecular condensates compartmentalize and regulate assemblies of biomolecules engaged in vital physiological processes in cells. Specific proteins and nucleic acids engaged in shared functions occur in any one kind of condensate, suggesting that ... ...

    Abstract Biomolecular condensates compartmentalize and regulate assemblies of biomolecules engaged in vital physiological processes in cells. Specific proteins and nucleic acids engaged in shared functions occur in any one kind of condensate, suggesting that these compartments have distinct chemical specificities. Indeed, some small-molecule drugs concentrate in specific condensates due to chemical properties engendered by particular amino acids in the proteins in those condensates. Here we argue that the chemical properties that govern molecular interactions between a small molecule and biomolecules within a condensate can be ascertained for both the small molecule and the biomolecules. We propose that learning this 'chemical grammar', the rules describing the chemical features of small molecules that engender attraction or repulsion by the physicochemical environment of a specific condensate, should enable design of drugs with improved efficacy and reduced toxicity.
    MeSH term(s) Biomolecular Condensates ; Proteins/chemistry
    Chemical Substances Proteins
    Language English
    Publishing date 2022-06-27
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2202962-X
    ISSN 1552-4469 ; 1552-4450
    ISSN (online) 1552-4469
    ISSN 1552-4450
    DOI 10.1038/s41589-022-01046-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Disulfide Chromophores Arise from Stereoelectronic Effects.

    Kilgore, Henry R / Raines, Ronald T

    The journal of physical chemistry. B

    2020  Volume 124, Issue 19, Page(s) 3931–3935

    Abstract: Bonds between sulfur atoms are prevalent in natural products, peptides, and proteins. Disulfide bonds have a distinct chromophore. The wavelength of their maximal absorbance varies widely, from 250 to 500 nm. Here, we demonstrate that this wavelength ... ...

    Abstract Bonds between sulfur atoms are prevalent in natural products, peptides, and proteins. Disulfide bonds have a distinct chromophore. The wavelength of their maximal absorbance varies widely, from 250 to 500 nm. Here, we demonstrate that this wavelength derives from stereoelectronic effects and is predictable using quantum chemistry. We also provide a sinusoidal equation, analogous to the Karplus equation, that relates the absorbance maximum and the C-S-S-C dihedral angle. These insights provide a facile means to characterize important attributes of disulfide bonds and to design disulfides with specified photophysical properties.
    MeSH term(s) Disulfides ; Peptides ; Protein Domains ; Proteins
    Chemical Substances Disulfides ; Peptides ; Proteins
    Language English
    Publishing date 2020-05-05
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.0c02272
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: n→π* Interactions Modulate the Properties of Cysteine Residues and Disulfide Bonds in Proteins.

    Kilgore, Henry R / Raines, Ronald T

    Journal of the American Chemical Society

    2018  Volume 140, Issue 50, Page(s) 17606–17611

    Abstract: Noncovalent interactions are ubiquitous in biology, taking on roles that include stabilizing the conformation of and assembling biomolecules, and providing an optimal environment for enzymatic catalysis. Here, we describe a noncovalent interaction that ... ...

    Abstract Noncovalent interactions are ubiquitous in biology, taking on roles that include stabilizing the conformation of and assembling biomolecules, and providing an optimal environment for enzymatic catalysis. Here, we describe a noncovalent interaction that engages the sulfur atoms of cysteine residues and disulfide bonds in proteins-their donation of electron density into an antibonding orbital of proximal amide carbonyl groups. This n→ π* interaction tunes the reactivity of the CXXC motif, which is the critical feature of thioredoxin and other enzymes involved in redox homeostasis. In particular, an n→ π* interaction lowers the p K
    MeSH term(s) Amino Acid Motifs ; Animals ; Aspergillus/enzymology ; Bacteria/enzymology ; Bacterial Proteins/chemistry ; Catalytic Domain ; Computational Biology ; Computer Simulation ; Cysteine/chemistry ; Disulfides/chemistry ; Drosophila melanogaster/chemistry ; Enzymes/chemistry ; Fungal Proteins/chemistry ; Humans ; Hydrogen Bonding ; Models, Chemical ; Protein Conformation ; Proteins/chemistry ; Static Electricity
    Chemical Substances Bacterial Proteins ; Disulfides ; Enzymes ; Fungal Proteins ; Proteins ; Cysteine (K848JZ4886)
    Language English
    Publishing date 2018-12-06
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 3155-0
    ISSN 1520-5126 ; 0002-7863
    ISSN (online) 1520-5126
    ISSN 0002-7863
    DOI 10.1021/jacs.8b09701
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Chemical codes promote selective compartmentalization of proteins.

    Kilgore, Henry R / Chinn, Itamar / Mikhael, Peter G / Mitnikov, Ilan / Van Dongen, Catherine / Zylberberg, Guy / Afeyan, Lena / Banani, Salman / Wilson-Hawken, Susana / Lee, Tong Ihn / Barzilay, Regina / Young, Richard A

    bioRxiv : the preprint server for biology

    2024  

    Abstract: Cells have evolved mechanisms to distribute ~10 billion protein molecules to subcellular compartments where diverse proteins involved in shared functions must efficiently assemble. Such assembly is presumed to unfold as a result of specific interactions ... ...

    Abstract Cells have evolved mechanisms to distribute ~10 billion protein molecules to subcellular compartments where diverse proteins involved in shared functions must efficiently assemble. Such assembly is presumed to unfold as a result of specific interactions between biomolecules; however, recent evidence suggests that distinctive chemical environments within subcellular compartments may also play an important role. Here, we test the hypothesis that protein groups with shared functions also share codes that guide them to compartment destinations. To test our hypothesis, we developed a transformer large language model, called ProtGPS, that predicts with high performance the compartment localization of human proteins excluded from the training set. We then demonstrate ProtGPS can be used for guided generation of novel protein sequences that selectively assemble into specific compartments in cells. Furthermore, ProtGPS predictions were sensitive to disease-associated mutations that produce changes in protein compartmentalization, suggesting that this type of pathogenic dysfunction can be discovered in silico. Our results indicate that protein sequences contain not only a folding code, but also a previously unrecognized chemical code governing their distribution in specific cellular compartments.
    Language English
    Publishing date 2024-04-15
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.04.15.589616
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: n→π* Interactions Modulate the Properties of Cysteine Residues and Disulfide Bonds in Proteins

    Kilgore, Henry R / Raines, Ronald T

    Journal of the American Chemical Society. 2018 Nov. 07, v. 140, no. 50

    2018  

    Abstract: Noncovalent interactions are ubiquitous in biology, taking on roles that include stabilizing the conformation of and assembling biomolecules, and providing an optimal environment for enzymatic catalysis. Here, we describe a noncovalent interaction that ... ...

    Abstract Noncovalent interactions are ubiquitous in biology, taking on roles that include stabilizing the conformation of and assembling biomolecules, and providing an optimal environment for enzymatic catalysis. Here, we describe a noncovalent interaction that engages the sulfur atoms of cysteine residues and disulfide bonds in proteins—their donation of electron density into an antibonding orbital of proximal amide carbonyl groups. This n→π* interaction tunes the reactivity of the CXXC motif, which is the critical feature of thioredoxin and other enzymes involved in redox homeostasis. In particular, an n→π* interaction lowers the pKa value of the N-terminal cysteine residue of the motif, which is the nucleophile that initiates catalysis. In addition, the interplay between disulfide n→π* interactions and C5 hydrogen bonds leads to hyperstable β-strands. Finally, n→π* interactions stabilize vicinal disulfide bonds, which are naturally diverse in function. These previously unappreciated n→π* interactions are strong and underlie the ability of cysteine residues and disulfide bonds to engage in the structure and function of proteins.
    Keywords Lewis bases ; catalytic activity ; cysteine ; disulfide bonds ; homeostasis ; hydrogen bonding ; moieties ; proteins ; sulfur ; thioredoxins
    Language English
    Dates of publication 2018-1107
    Size p. 17606-17611.
    Publishing place American Chemical Society
    Document type Article
    ZDB-ID 3155-0
    ISSN 1520-5126 ; 0002-7863
    ISSN (online) 1520-5126
    ISSN 0002-7863
    DOI 10.1021/jacs.8b09701
    Database NAL-Catalogue (AGRICOLA)

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  6. Article: Structure and Dynamics of N-Glycosylated Human Ribonuclease 1

    Kilgore, Henry R / Latham, Andrew P / Ressler, Valerie T / Zhang, Bin / Raines, Ronald T

    Biochemistry. 2020 June 16, v. 59, no. 34

    2020  

    Abstract: Glycosylation is a common modification that can endow proteins with altered physical and biological properties. Ribonuclease 1 (RNase 1), which is the human homologue of the archetypal enzyme RNase A, undergoes N-linked glycosylation at asparagine ... ...

    Abstract Glycosylation is a common modification that can endow proteins with altered physical and biological properties. Ribonuclease 1 (RNase 1), which is the human homologue of the archetypal enzyme RNase A, undergoes N-linked glycosylation at asparagine residues 34, 76, and 88. We have produced the three individual glycoforms that display the core heptasaccharide, Man₅GlcNAc₂, and analyzed the structure of each glycoform by using small-angle X-ray scattering along with molecular dynamics simulations. The glycan on Asn34 is relatively compact and rigid, donates hydrogen bonds that “cap” the carbonyl groups at the C-terminus of an α-helix, and enhances protein thermostability. In contrast, the glycan on Asn88 is flexible and can even enter the enzymic active site, hindering catalysis. The N-glycosylation of Asn76 has less pronounced consequences. These data highlight the diverse behaviors of Man₅GlcNAc₂ pendants and provide a structural underpinning to the functional consequences of protein glycosylation.
    Keywords active sites ; asparagine ; catalytic activity ; dynamics ; glycosylation ; humans ; hydrogen bonding ; molecular dynamics ; proteins ; ribonucleases ; small-angle X-ray scattering ; thermal stability
    Language English
    Dates of publication 2020-0616
    Size p. 3148-3156.
    Publishing place American Chemical Society
    Document type Article
    Note NAL-light
    ZDB-ID 1108-3
    ISSN 1520-4995 ; 0006-2960
    ISSN (online) 1520-4995
    ISSN 0006-2960
    DOI 10.1021/acs.biochem.0c00191
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  7. Article ; Online: Cytosolic Uptake of Large Monofunctionalized Dextrans.

    Chyan, Wen / Kilgore, Henry R / Raines, Ronald T

    Bioconjugate chemistry

    2018  Volume 29, Issue 6, Page(s) 1942–1949

    Abstract: Dextrans are a versatile class of polysaccharides with applications that span medicine, cell biology, food science, and consumer goods. Here, we report on a new type of large monofunctionalized dextran that exhibits unusual properties: efficient ... ...

    Abstract Dextrans are a versatile class of polysaccharides with applications that span medicine, cell biology, food science, and consumer goods. Here, we report on a new type of large monofunctionalized dextran that exhibits unusual properties: efficient cytosolic and nuclear uptake. This dextran permeates various human cell types without the use of transfection agents, electroporation, or membrane perturbation. Cellular uptake occurs primarily through active transport via receptor-mediated processes. These monofunctionalized dextrans could serve as intracellular delivery platforms for drugs or other cargos.
    MeSH term(s) Biological Transport ; Cell Line ; Cell Nucleus/metabolism ; Cytosol/metabolism ; Dextrans/chemistry ; Dextrans/pharmacokinetics ; Drug Carriers/chemistry ; Drug Carriers/pharmacokinetics ; HeLa Cells ; Humans ; Models, Molecular
    Chemical Substances Dextrans ; Drug Carriers
    Language English
    Publishing date 2018-04-25
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1024041-x
    ISSN 1520-4812 ; 1043-1802
    ISSN (online) 1520-4812
    ISSN 1043-1802
    DOI 10.1021/acs.bioconjchem.8b00198
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    Zs.A 3400: Show issues Location:
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  8. Article ; Online: n

    Kilgore, Henry R / Olsson, Chase R / D'Angelo, Kyan A / Movassaghi, Mohammad / Raines, Ronald T

    Journal of the American Chemical Society

    2020  Volume 142, Issue 35, Page(s) 15107–15115

    Abstract: Epithiodiketopiperazines (ETPs) are a structurally complex class of fungal natural products with potent anticancer activity. In ETPs, the diketopiperazine ring is spanned by a disulfide bond that is constrained in a high-energy eclipsed conformation. We ... ...

    Abstract Epithiodiketopiperazines (ETPs) are a structurally complex class of fungal natural products with potent anticancer activity. In ETPs, the diketopiperazine ring is spanned by a disulfide bond that is constrained in a high-energy eclipsed conformation. We employed computational, synthetic, and spectroscopic methods to investigate the physicochemical attributes of this atypical disulfide bond. We find that the disulfide bond is stabilized by two
    MeSH term(s) Crystallography, X-Ray ; Density Functional Theory ; Disulfides/chemistry ; Models, Molecular ; Molecular Structure ; Oxidation-Reduction ; Piperazines/chemistry ; Thermodynamics
    Chemical Substances Disulfides ; Piperazines ; epidithiodiketopiperazine
    Language English
    Publishing date 2020-08-21
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 3155-0
    ISSN 1520-5126 ; 0002-7863
    ISSN (online) 1520-5126
    ISSN 0002-7863
    DOI 10.1021/jacs.0c06477
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Structure and Dynamics of N-Glycosylated Human Ribonuclease 1.

    Kilgore, Henry R / Latham, Andrew P / Ressler, Valerie T / Zhang, Bin / Raines, Ronald T

    Biochemistry

    2020  Volume 59, Issue 34, Page(s) 3148–3156

    Abstract: Glycosylation is a common modification that can endow proteins with altered physical and biological properties. Ribonuclease 1 (RNase 1), which is the human homologue of the archetypal enzyme RNase A, undergoes N-linked glycosylation at asparagine ... ...

    Abstract Glycosylation is a common modification that can endow proteins with altered physical and biological properties. Ribonuclease 1 (RNase 1), which is the human homologue of the archetypal enzyme RNase A, undergoes N-linked glycosylation at asparagine residues 34, 76, and 88. We have produced the three individual glycoforms that display the core heptasaccharide, Man
    MeSH term(s) Catalytic Domain ; Glycosylation ; Humans ; Models, Molecular ; Nitrogen/metabolism ; Ribonucleases/chemistry ; Ribonucleases/metabolism
    Chemical Substances Ribonucleases (EC 3.1.-) ; Nitrogen (N762921K75)
    Language English
    Publishing date 2020-06-30
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1108-3
    ISSN 1520-4995 ; 0006-2960
    ISSN (online) 1520-4995
    ISSN 0006-2960
    DOI 10.1021/acs.biochem.0c00191
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  10. Article ; Online: Author Correction: Distinct chemical environments in biomolecular condensates.

    Kilgore, Henry R / Mikhael, Peter G / Overholt, Kalon J / Boija, Ann / Hannett, Nancy M / Van Dongen, Catherine / Lee, Tong Ihn / Chang, Young-Tae / Barzilay, Regina / Young, Richard A

    Nature chemical biology

    2023  Volume 19, Issue 12, Page(s) 1561

    Language English
    Publishing date 2023-10-26
    Publishing country United States
    Document type Published Erratum
    ZDB-ID 2202962-X
    ISSN 1552-4469 ; 1552-4450
    ISSN (online) 1552-4469
    ISSN 1552-4450
    DOI 10.1038/s41589-023-01491-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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