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  1. Article: Non-covalent interactions in biomacromolecules.

    Cerný, Jirí / Hobza, Pavel

    Physical chemistry chemical physics : PCCP

    2007  Volume 9, Issue 39, Page(s) 5291–5303

    Abstract: Non-covalent interactions play an important role in chemistry, physics and especially ... in biodisciplines. They determine the structure of biomacromolecules such as DNA and proteins and are responsible ... is covered (e.g. by performing CCSD(T) calculations). The role of H-bonding and stacking interactions ...

    Abstract Non-covalent interactions play an important role in chemistry, physics and especially in biodisciplines. They determine the structure of biomacromolecules such as DNA and proteins and are responsible for the molecular recognition process. Theoretical evaluation of interaction energies is difficult; however, perturbation as well as variation (supermolecular) methods are briefly described. Accurate interaction energies can be obtained by complete basis set limit calculations providing a large portion of correlation energy is covered (e.g. by performing CCSD(T) calculations). The role of H-bonding and stacking interactions in the stabilisation of DNA, oligopeptides and proteins is described, and the importance of London dispersion energy is shown.
    MeSH term(s) Base Pairing ; DNA/chemistry ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Nucleic Acid Conformation ; Proteins/chemistry ; Thermodynamics
    Chemical Substances Proteins ; DNA (9007-49-2)
    Language English
    Publishing date 2007-10-21
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1476244-4
    ISSN 1463-9084 ; 1463-9076
    ISSN (online) 1463-9084
    ISSN 1463-9076
    DOI 10.1039/b704781a
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Non-Covalent Carrier Hydrophobicity as a Universal Predictor of Intracellular Protein Activity.

    Hango, Christopher R / Backlund, Coralie M / Davis, Hazel C / Posey, Nicholas D / Minter, Lisa M / Tew, Gregory N

    Biomacromolecules

    2021  Volume 22, Issue 7, Page(s) 2850–2863

    Abstract: ... for non-covalent protein delivery, namely, poly(alanine- ... the need for covalent conjugation often required by CPPs. In this study, design rules learned from CPPM ...

    Abstract Over the past decade, extensive optimization of polymeric cell-penetrating peptide (CPP) mimics (CPPMs) by our group has generated a substantial library of broadly effective carriers which circumvent the need for covalent conjugation often required by CPPs. In this study, design rules learned from CPPM development were applied to reverse-engineer the first library of simple amphiphilic block copolypeptides for non-covalent protein delivery, namely, poly(alanine-
    MeSH term(s) Biological Transport ; Cell-Penetrating Peptides/metabolism ; Hydrophobic and Hydrophilic Interactions ; Polymers ; Protein Transport
    Chemical Substances Cell-Penetrating Peptides ; Polymers
    Language English
    Publishing date 2021-06-22
    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 1526-4602
    ISSN (online) 1526-4602
    DOI 10.1021/acs.biomac.1c00242
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Non-covalent interactions in anisole-(CO

    Becucci, Maurizio / Mazzoni, Federico / Pietraperzia, Giangaetano / Řezáč, Jan / Natchigallová, Dana / Hobza, Pavel

    Physical chemistry chemical physics : PCCP

    2017  Volume 19, Issue 34, Page(s) 22749–22758

    Abstract: Non-covalent interactions are ubiquitous and represent a very important binding motif. The direct ... its importance, for instance, for understanding and predicting the structure of bio-macromolecules. Here ...

    Abstract Non-covalent interactions are ubiquitous and represent a very important binding motif. The direct experimental measurement of binding energies in complexes has been elusive for a long time despite its importance, for instance, for understanding and predicting the structure of bio-macromolecules. Here, we report a combined experimental and computational analysis on the 1 : 1 and 1 : 2 clusters formed by anisole (methoxybenzene) and carbon dioxide molecules. We have obtained a detailed description of the interaction between CO
    Language English
    Publishing date 2017-08-30
    Publishing country England
    Document type Journal Article
    ZDB-ID 1476244-4
    ISSN 1463-9084 ; 1463-9076
    ISSN (online) 1463-9084
    ISSN 1463-9076
    DOI 10.1039/c7cp03763e
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Applying mass spectrometry to study non-covalent biomolecule complexes.

    Chen, Fan / Gülbakan, Basri / Weidmann, Simon / Fagerer, Stephan R / Ibáñez, Alfredo J / Zenobi, Renato

    Mass spectrometry reviews

    2016  Volume 35, Issue 1, Page(s) 48–70

    Abstract: Non-covalent interactions are essential for the structural organization of biomacromolecules and ... MS is heavily used in studies of non-covalent interactions and to understand the architecture ... the intact complex without fragmentation when analyzing non-covalent interactions with MALDI-MS. There are ...

    Abstract Non-covalent interactions are essential for the structural organization of biomacromolecules and play an important role in molecular recognition processes, such as the interactions between proteins, glycans, lipids, DNA, and RNA. Mass spectrometry (MS) is a powerful tool for studying of non-covalent interactions, due to the low sample consumption, high sensitivity, and label-free nature. Nowadays, native-ESI MS is heavily used in studies of non-covalent interactions and to understand the architecture of biomolecular complexes. However, MALDI-MS is also becoming increasingly useful. It is challenging to detect the intact complex without fragmentation when analyzing non-covalent interactions with MALDI-MS. There are two methodological approaches to do so. In the first approach, different experimental and instrumental parameters are fine-tuned in order to find conditions under which the complex is stable, such as applying non-acidic matrices and collecting first-shot spectra. In the second approach, the interacting species are "artificially" stabilized by chemical crosslinking. Both approaches are capable of studying non-covalently bound biomolecules even in quite challenging systems, such as membrane protein complexes. Herein, we review and compare native-ESI and MALDI MS for the study of non-covalent interactions.
    MeSH term(s) Biochemistry/methods ; Biophysics/methods ; Cross-Linking Reagents/chemistry ; Crystallography, X-Ray/methods ; Glutaral/chemistry ; Mass Spectrometry/methods ; Multiprotein Complexes/analysis ; Multiprotein Complexes/chemistry ; Spectrometry, Mass, Electrospray Ionization/methods ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
    Chemical Substances Cross-Linking Reagents ; Multiprotein Complexes ; Glutaral (T3C89M417N)
    Language English
    Publishing date 2016-01
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 1491946-1
    ISSN 1098-2787 ; 0277-7037
    ISSN (online) 1098-2787
    ISSN 0277-7037
    DOI 10.1002/mas.21462
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: The n → π* interaction: a rapidly emerging non-covalent interaction.

    Singh, Santosh K / Das, Aloke

    Physical chemistry chemical physics : PCCP

    2015  Volume 17, Issue 15, Page(s) 9596–9612

    Abstract: ... important to other non-covalent interactions for the stability and specific structures of biomolecules and ... which other commonly known non-covalent interactions (conventional hydrogen bonding, π-hydrogen bonding, π-stacking ... This perspective describes the current status of a recently discovered non-covalent interaction ...

    Abstract This perspective describes the current status of a recently discovered non-covalent interaction named as the n → π* interaction, which is very weak and counterintuitive in nature. In this review, we have provided a brief overview of the widespread presence of this interaction in biomacromolecules, small biomolecules and materials, as well as the physical nature of this interaction explored using various experimental and theoretical techniques. It has been found that this interaction is equally important to other non-covalent interactions for the stability and specific structures of biomolecules and materials. An in-depth understanding of this interaction can help in designing more efficient functional materials as well as drugs. The review also provides a future outlook in terms of exploring the detailed functional role of this interaction in biological processes and its direct spectroscopic evidence, which other commonly known non-covalent interactions (conventional hydrogen bonding, π-hydrogen bonding, π-stacking, etc.) have.
    MeSH term(s) Hydrogen Bonding ; Models, Biological ; Quantum Theory ; Spectrum Analysis
    Language English
    Publishing date 2015-04-21
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1476244-4
    ISSN 1463-9084 ; 1463-9076
    ISSN (online) 1463-9084
    ISSN 1463-9076
    DOI 10.1039/c4cp05536e
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Non-covalent loading of ionic liquid-functionalized nanoparticles for bovine serum albumin: experiments and theoretical analysis

    Jia, Xingang / Hu, Xiaoling / Wang, Wenzhen / Du, Chunbao

    RSC advances. 2019 June 18, v. 9, no. 33

    2019  

    Abstract: ... functionalized nanoparticles (SiO2@IL) using surface grafting technology. By employing multiple non-covalent ... Biomacromolecule-based nanomaterials have attracted much attention due to their excellent function ... demonstrated that it is promising in applications for biomacromolecule immobilization. ...

    Abstract Biomacromolecule-based nanomaterials have attracted much attention due to their excellent function in sensing, catalysis, medicine, biology and recognition. In this work, a silane-coupling ionic liquid, 1-(3-trimethoxysilylpropyl)-3-methylimidazolium chloride ([TMIM]Cl), was synthesized and applied to prepare ionic liquid-functionalized nanoparticles (SiO2@IL) using surface grafting technology. By employing multiple non-covalent interactions, including electrostatic interactions, hydrogen bonding and π–π stacking, the obtained functional nanoparticles were able to bind bovine serum albumin (BSA) with strong binding affinity, which has been illustrated through experiments and theoretical calculations. Moreover, the stability of SiO2@IL further demonstrated that it is promising in applications for biomacromolecule immobilization.
    Keywords binding capacity ; bovine serum albumin ; catalytic activity ; electrostatic interactions ; hydrogen bonding ; ionic liquids ; medicine ; nanoparticles ; silica
    Language English
    Dates of publication 2019-0618
    Size p. 19114-19120.
    Publishing place The Royal Society of Chemistry
    Document type Article
    ISSN 2046-2069
    DOI 10.1039/c9ra02265a
    Database NAL-Catalogue (AGRICOLA)

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  7. Article: Multi-responsive polyethylene-polyamine/gelatin hydrogel induced by non-covalent interactions

    Zhang, Zhidong / Liu, Yingxin / Chen, Xin / Shao, Zhengzhong

    RSC advances. 2016 May 18, v. 6, no. 54

    2016  

    Abstract: ... non-covalent interactions, which were able to provide various stimuli-responsiveness such as stress ... to other biomacromolecule based hydrogel adhesives, while it held more stimuli-responsiveness properties ...

    Abstract By simply introducing a gelatin aqueous solution, the polyethylene-polyamine (PPA)/gelatin hydrogel with multi-stimuli-responsive properties was obtained. It was demonstrated that the hydrogel was formed via non-covalent interactions, which were able to provide various stimuli-responsiveness such as stress, pH and thermal/photo-thermal to the hydrogel. Furthermore, the adhesion experiment revealed that the hydrogel was similar in adhesive strength but more convenient in preparation compared to other biomacromolecule based hydrogel adhesives, while it held more stimuli-responsiveness properties. Therefore, such a general strategy of the PPA based hydrogel preparation displayed its great potential to design smart materials for multi-functional applications.
    Keywords adhesion ; adhesives ; aqueous solutions ; gelatin ; hydrogels ; pH
    Language English
    Dates of publication 2016-0518
    Size p. 48661-48665.
    Publishing place The Royal Society of Chemistry
    Document type Article
    ISSN 2046-2069
    DOI 10.1039/c6ra05764k
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  8. Article: In vitro evaluation of the non-covalent interactions of hemoglobin with distinctively modified gemini surfactants: Effect of structural variation

    Akram, Mohd / Imtiyaz Ahmad Bhat / Kabir-ud-Din / Sana Anwar

    Colloids and surfaces. 2017 Aug. 20, v. 527

    2017  

    Abstract: Binding of surfactants to biomacromolecules is an active field of current interest at the interface ... cosmetic domains. In relevance to this, we have investigated the interactions of two distinctly modified ...

    Abstract Binding of surfactants to biomacromolecules is an active field of current interest at the interface of chemical biology and medicinal chemistry, owing to their diverse applications in industries, biomedical and cosmetic domains. In relevance to this, we have investigated the interactions of two distinctly modified green gemini surfactants (C12-E2O-C12 and C14-E2O-C14) with the heme protein hemoglobin (Hb) utilizing different state-of-the-art techniques. These surfactants are employed to explicate the effect of structural variation on the conformation of Hb. Complexation between Hb and C12-E2O-C12/C14-E2O-C14 were found to follow the same 1:1 stoichiometric pattern but with different binding constants (evaluated through fluorescence and electrochemical measurements). The UV–vis spectra showed the influence of C12-E2O-C12/C14-E2O-C14 on Hb, displaying a strong concentration-dependent fashion. Furthermore, pyrene, synchronous and 3-D fluorescence spectra of Hb depicted the possible alterations induced in its aromatic microenvironment upon C12-E2O-C12/C14-E2O-C14 complexation. Far-UV CD results revealed nominal changes in the secondary structure of the Hb while a considerable loss in tertiary structure was observed in the near-UV range, elucidating the formation of molten globule state. The best energy-docked structure in the molecular docking analysis revealed that C12-E2O-C12/C14-E2O-C14 preferred to bind in the hydrophobic cavity of Hb. Thus, this work provides a comprehensive inspection of Hb-C12-E2O-C12/C14-E2O-C14 interaction at the molecular level that can be extended potentially to other congeners, which is essential in determining their future use as excipients in pharmaceutical formulations and other related applications.
    Keywords drug formulations ; electrochemistry ; fluorescence ; fluorescence emission spectroscopy ; heme ; hemoglobin ; hydrophobicity ; in vitro studies ; industry ; molecular models ; surfactants
    Language English
    Dates of publication 2017-0820
    Size p. 145-157.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 1500517-3
    ISSN 0927-7757
    ISSN 0927-7757
    DOI 10.1016/j.colsurfa.2017.05.021
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  9. Article: [Application and development of spectroscopy methodologies in the study on non-covalent interactions].

    Li, Rui / Dai, Ben-Cai / Zhao, Yong-De / Lu, Kui

    Guang pu xue yu guang pu fen xi = Guang pu

    2009  Volume 29, Issue 1, Page(s) 240–243

    Abstract: ... methodologies in the study of non-covalent interactions between small-molecule and biomacromolecule is ... and non-covalent interactions study for its convenience and speed. In the present paper, spectroscopy ... of common spectroscopy methodologies in the study of non-covalent interactions between small molecule and ...

    Abstract Spectrophotometric method is widely used in the structure determination of biologic macromolecules and non-covalent interactions study for its convenience and speed. In the present paper, spectroscopy methodologies in the study of non-covalent interactions between small-molecule and biomacromolecule is comprehensively reviewed with 25 references. This review article focuses on the applications and development of common spectroscopy methodologies in the study of non-covalent interactions between small molecule and biomacromolecule,including the UV, fluorescence, CD, IR, Raman, resonance light scattering technique and SPR. The advantages and disadvantages of spectroscopy methodologies are also described. UV-Vis absorption spectrum (UV) method is widely used in the study of non-covalent interactions for its convenience and speed. The binding site number, the apparent binding constant and the interaction mode of non-covalent interactions can be obtained by fluorescence spectrum method. Circular dichroism (CD) method is effective way in the study of non-covalent interactions measure. Spectroscopy information about protein secondary structure and conformation can be acquired by infrared spectrometry (IR) method. Raman spectroscopy method is a better way to investigate the conformation change in macromolecules in solution. Non-covalent interactions can be measured by surface plasma resonance (SPR) method under the natural active condition. X-ray diffraction analysis method is better for non-covalent interactions research, but it is difficult to cultivate crystalline complex.
    Language Chinese
    Publishing date 2009-01
    Publishing country China
    Document type English Abstract ; Journal Article
    ISSN 1000-0593
    ISSN 1000-0593
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Single chain folding of synthetic polymers by covalent and non-covalent interactions: current status and future perspectives.

    Altintas, Ozcan / Barner-Kowollik, Christopher

    Macromolecular rapid communications

    2012  Volume 33, Issue 11, Page(s) 958–971

    Abstract: ... defined linear polymers through covalent and non-covalent interactions. Initially, the discussion focuses ... on the synthesis and characterization of single chain self-folded structures by non-covalent interactions ... attempts towards mimicking the structure of natural biomacromolecules by single chain folding of well ...

    Abstract The present feature article highlights the preparation of polymeric nanoparticles and initial attempts towards mimicking the structure of natural biomacromolecules by single chain folding of well-defined linear polymers through covalent and non-covalent interactions. Initially, the discussion focuses on the synthesis and characterization of single chain self-folded structures by non-covalent interactions. The second part of the article summarizes the folding of single chain polymers by means of covalent interactions into nanoparticle systems. The current state of the art in the field of single chain folding indicates that covalent-bond-driven nanoparticle preparation is well advanced, while the first encouraging steps towards building reversible single chain folding systems by the use of mutually orthogonal hydrogen-bonding motifs have been made.
    MeSH term(s) Biomimetic Materials/chemistry ; Models, Chemical ; Nanoparticles/chemistry ; Polymers/chemistry
    Chemical Substances Polymers
    Language English
    Publishing date 2012-06-14
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1475027-2
    ISSN 1521-3927 ; 1022-1336
    ISSN (online) 1521-3927
    ISSN 1022-1336
    DOI 10.1002/marc.201200049
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