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Bregnhøj M, Golbek TW, Madzharova F, Weidner T. De Novo Design and Characterization of Amphiphilic Peptides with Basic Side Chains for Tailored Interfacial Chemistries. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:19404-19411. [PMID: 39213639 DOI: 10.1021/acs.langmuir.4c01654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Lysine-leucine (LK) peptides have been used as model systems and platforms for 2D material design for decades. LK peptides are amphiphilic sequences designed to bind and fold at hydrophobic surfaces through hydrophobic leucine side chains and hydrophilic lysine side chains extending into the aqueous subphase. The hydrophobic periodicity of the sequence dictates the secondary structure at the interface. This robust design makes them ideal candidates for controlling interfacial chemistry. This study presents the de novo design and characterization of two novel peptides: LRα14 and LHα14, which substitute lysine with arginine and histidine, respectively, in the helical LKα14 sequence. This modification is intended to expand the LK peptide platform to a new basic interfacial chemistry. We explore the stability of the new LRα14 and LHα14 designs with respect to changes in pH and salt concentration in bulk solution and at the interface using circular dichroism (UV-CD) and vibrational sum-frequency generation spectroscopy, respectively. Notably, the structural stability of the peptides remains unaffected across a wide range of pH and ionic strength values. At the same time, the variation of side-chain chemistry leads to a wide spectrum of interfacial water structures. By extension of the LK platform to include arginine and histidine, this study broadens the toolbox for designing tailored interfacial chemistries with applications in material and biomedical sciences.
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Affiliation(s)
- Mikkel Bregnhøj
- Department of Chemistry, Aarhus University, 8000 Aarhus, Denmark
| | | | - Fani Madzharova
- Department of Chemistry, Aarhus University, 8000 Aarhus, Denmark
| | - Tobias Weidner
- Department of Chemistry, Aarhus University, 8000 Aarhus, Denmark
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2
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Perets EA, Konstantinovsky D, Santiago T, Videla PE, Tremblay M, Velarde L, Batista VS, Hammes-Schiffer S, Yan ECY. Beyond the "spine of hydration": Chiral SFG spectroscopy detects DNA first hydration shell and base pair structures. J Chem Phys 2024; 161:095104. [PMID: 39230381 PMCID: PMC11377083 DOI: 10.1063/5.0220479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Accepted: 08/06/2024] [Indexed: 09/05/2024] Open
Abstract
Experimental methods capable of selectively probing water at the DNA minor groove, major groove, and phosphate backbone are crucial for understanding how hydration influences DNA structure and function. Chiral-selective sum frequency generation spectroscopy (chiral SFG) is unique among vibrational spectroscopies because it can selectively probe water molecules that form chiral hydration structures around biomolecules. However, interpreting chiral SFG spectra is challenging since both water and the biomolecule can produce chiral SFG signals. Here, we combine experiment and computation to establish a theoretical framework for the rigorous interpretation of chiral SFG spectra of DNA. We demonstrate that chiral SFG detects the N-H stretch of DNA base pairs and the O-H stretch of water, exclusively probing water molecules in the DNA first hydration shell. Our analysis reveals that DNA transfers chirality to water molecules only within the first hydration shell, so they can be probed by chiral SFG spectroscopy. Beyond the first hydration shell, the electric field-induced water structure is symmetric and, therefore, precludes chiral SFG response. Furthermore, we find that chiral SFG can differentiate chiral subpopulations of first hydration shell water molecules at the minor groove, major groove, and phosphate backbone. Our findings challenge the scientific perspective dominant for more than 40 years that the minor groove "spine of hydration" is the only chiral water structure surrounding the DNA double helix. By identifying the molecular origins of the DNA chiral SFG spectrum, we lay a robust experimental and theoretical foundation for applying chiral SFG to explore the chemical and biological physics of DNA hydration.
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Affiliation(s)
- Ethan A Perets
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Daniel Konstantinovsky
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Ty Santiago
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Pablo E Videla
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Matthew Tremblay
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Luis Velarde
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260, USA
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Elsa C Y Yan
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
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3
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Dean JLS, Cramer CG, Fournier JA. Interplay between anion-receptor and anion-solvent interactions in halide receptor complexes characterized with ultrafast infrared spectroscopies. Phys Chem Chem Phys 2024; 26:21163-21172. [PMID: 39072495 DOI: 10.1039/d4cp02280g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
The competition between host-guest binding and solvent interactions is a crucial factor in determining the binding affinities and selectivity of molecular receptor species. The interplay between these competing interactions, however, have been difficult to disentangle. In particular, the development of molecular-level descriptions of solute-solvent interactions remains a grand experimental challenge. Herein, we investigate the prototypical halide receptor meso-octamethylcalix[4]pyrrole (OMCP) complexed with either chloride or bromide anions in both dichloromethane (DCM) and chloroform (trichloromethane, TCM) solvent using ultrafast infrared transient absorption and 2D IR spectroscopies. OMCP·Br- complexes in both solvents display slower vibrational relaxation dynamics of the OMCP pyrrole NH stretches, consistent with weaker H-bonding interactions with OMCP compared to chloride and less efficient intermolecular relaxation to the solvent. Further, OMCP·Br- complexes show nearly static spectral diffusion dynamics compared to OMCP·Cl-, indicating larger structural fluctuations occur within chloride complexes. Importantly, distinct differences in the vibrational spectra and dynamics are observed between DCM and TCM solutions. The data are consistent with stronger and more perturbative solvent effects in TCM compared to DCM, despite DCM's larger dielectric constant and smaller reported OMCP·X- binding affinities. These differences are attributed to the presence of weak H-bond interactions between halides and TCM, in addition to competing interactions from the bulky tetrabutylammonium countercation. The data provide important experimental benchmarks for quantifying the role of solvent and countercation interactions in anion host-guest complexes.
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Affiliation(s)
- Jessika L S Dean
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA.
| | - Caroline G Cramer
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA.
| | - Joseph A Fournier
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA.
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4
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Rajpersaud T, Tabandeh S, Leon L, Loverde SM. Molecular Dynamics Simulations of Polyelectrolyte Complexes. Biomacromolecules 2024; 25:1468-1480. [PMID: 38366971 DOI: 10.1021/acs.biomac.3c01032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
Polyelectrolyte complexes (PECs) are currently of great interest due to their applications toward developing new adaptive materials and their relevance in membraneless organelles. These complexes emerge during phase separation when oppositely charged polymers are mixed in aqueous media. Peptide-based PECs are particularly useful toward developing new drug delivery methods due to their inherent biocompatibility. The underlying peptide sequence can be tuned to optimize specific material properties of the complex, such as interfacial tension and viscosity. Given their applicability, it would be advantageous to understand the underlying sequence-dependent phase behavior of oppositely charged peptides. Here, we report microsecond molecular dynamic simulations to characterize the effect of hydrophobicity on the sequence-dependent peptide conformation for model polypeptide sequences that were previously reported by Tabandeh et al. These sequences are designed with alternating chirality of the peptide backbone. We present microsecond simulations of six oppositely charged peptide pairs, characterizing the sequence-dependent effect on peptide size, degree of hydrogen bonding, secondary structure, and conformation. This analysis recapitulates sensible trends in peptide conformation and degree of hydrogen bonding, consistent with experimentally reported results. Ramachandran plots reveal that backbone conformation at the single amino acid level is highly influenced by the neighboring sequence in the chain. These results give insight into how subtle changes in hydrophobic side chain size and chirality influence the strength of hydrogen bonding between the chains and, ultimately, the secondary structure. Furthermore, principal component analysis reveals that the minimum energy structures may be subtly modulated by the underlying sequence.
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Affiliation(s)
- Tania Rajpersaud
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
| | - Sara Tabandeh
- Department of Materials Science and Engineering, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL 32816, United States
| | - Lorraine Leon
- Department of Materials Science and Engineering, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL 32816, United States
| | - Sharon M Loverde
- Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
- Department of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, NY 10314, United States
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, United States
- Ph.D. Program in Physics, The Graduate Center of the City University of New York, New York, NY 10016, United States
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5
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Noblet T, Busson B. Diagrammatic theory of magnetic and quadrupolar contributions to sum-frequency generation in composite systems. J Chem Phys 2024; 160:024704. [PMID: 38193549 DOI: 10.1063/5.0187520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 12/15/2023] [Indexed: 01/10/2024] Open
Abstract
Second-order nonlinear processes like Sum-Frequency Generation (SFG) are essentially defined in the electric dipolar approximation. However, when dealing with the SFG responses of bulk, big nanoparticles, highly symmetric objects, or chiral species, magnetic and quadrupolar contributions play a significant role in the process too. We extend the diagrammatic theory for linear and nonlinear optics to include these terms for single objects as well as for multipartite systems in interaction. Magnetic and quadrupolar quantities are introduced in the formalism as incoming fields, interaction intermediates, and sources of optical nonlinearity. New response functions and complex nonlinear processes are defined, and their symmetry properties are analyzed. This leads to a focus on several kinds of applications involving nanoscale coupled objects, symmetric molecular systems, and chiral materials, both in line with the existing literature and opening new possibilities for original complex systems.
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Affiliation(s)
- Thomas Noblet
- GRASP-Biophotonics, CESAM, University of Liege, Institute of Physics, Allée du 6 août 17, 4000 Liège, Belgium
| | - Bertrand Busson
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR 8000, 91405 Orsay, France
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6
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Yan ECY, Perets EA, Konstantinovsky D, Hammes-Schiffer S. Detecting Interplay of Chirality, Water, and Interfaces for Elucidating Biological Functions. Acc Chem Res 2023; 56:1494-1504. [PMID: 37163574 PMCID: PMC10344471 DOI: 10.1021/acs.accounts.3c00088] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Chemists have long been fascinated by chirality, water, and interfaces, making tremendous progress in each research area. However, the chemistry emerging from the interplay of chirality, water, and interfaces has been difficult to study due to technical challenges, creating a barrier to elucidating biological functions at interfaces. Most biopolymers (proteins, DNA, and RNA) fold into macroscopic chiral structures to perform biological functions. Their folding requires water, but water behaves differently at interfaces where the bulk water hydrogen-bonding network terminates. A question arises as to how water molecules rearrange to minimize free energy at interfaces while stabilizing the macroscopic folding of biopolymers to support biological function. This question is central to solving many research challenges, including the molecular origin of biological homochirality, folding and insertion of proteins into cell membranes, and the design of heterogeneous biocatalysts. Researchers can resolve these challenges if they have the theoretical tools to accurately predict molecular behaviors of water and biopolymers at various interfaces. However, developing such tools requires validation by the experimental data. These experimental data are scarce because few physical methods can simultaneously distinguish chiral folding of the biopolymers, separate signals of interfaces from the overwhelming background of bulk solvent, and differentiate water in hydration shells of the polymers from water elsewhere.We recently illustrated these very capacities of chirality-sensitive vibrational sum frequency generation spectroscopy (chiral SFG). While chiral SFG theory dictates that the method is surface-specific under the condition of electronic nonresonance, we show the method can distinguish chiral folding of proteins and DNA and probe water structures in the first hydration shell of proteins at interfaces. Using amide I signals, we observe protein folding into β-sheets without background signals from α-helices and disordered structures at interfaces, thereby demonstrating the effect of 2D crowding on protein folding. Also, chiral SFG signals of C-H stretches are silent from single-stranded DNA, but prominent for canonical antiparallel duplexes as well as noncanonical parallel duplexes at interfaces, allowing for sensing DNA secondary structures and hybridization. In establishing chiral SFG for detecting protein hydration structures, we observe an H218O isotopic shift that reveals water contribution to the chiral SFG spectra. Additionally, the phase of the O-H stretching bands flips when the protein chirality is switched from L to D. These experimental results agree with our simulated chiral SFG spectra of water hydrating the β-sheet protein at the vacuum-water interface. The simulations further reveal that over 90% of the total chiral SFG signal comes from water in the first hydration shell. We conclude that the chiral SFG signals originate from achiral water molecules that assemble around the protein into a chiral supramolecular structure with chirality transferred from the protein. As water O-H stretches can reveal hydrogen-bonding interactions, chiral SFG shows promise in probing the structures and dynamics of water-biopolymer interactions at interfaces. Altogether, our work has created an experimental and computational framework for chiral SFG to elucidate biological functions at interfaces, setting the stage for probing the intricate chemical interplay of chirality, water, and interfaces.
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Affiliation(s)
- Elsa C. Y. Yan
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Ethan A. Perets
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Daniel Konstantinovsky
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
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7
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Konstantinovsky D, Yan ECY, Hammes-Schiffer S. Characterizing Interfaces by Voronoi Tessellation. J Phys Chem Lett 2023; 14:5260-5266. [PMID: 37265175 PMCID: PMC10344600 DOI: 10.1021/acs.jpclett.3c01159] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The chemistry of interfaces differs markedly from that of the bulk. Calculation of interfacial properties depends strongly on the definition of the interface, which can lead to ambiguous results that vary between studies. There is a need for a method that can explicitly define the interfaces and boundaries in molecular systems. Voronoi tessellation offers an attractive solution to this problem through its ability to determine neighbors among specified groups of atoms. Here we discuss three cases where Voronoi tessellation combined with modeling of vibrational sum frequency generation (SFG) spectroscopy yields relevant insights: the breakdown of the air-water interface into clear and intuitive molecular layers, the study of the hydration shell in biological systems, and the acceleration of difficult spectral calculations where intermolecular vibrational couplings dominate. The utility of Voronoi tessellation has broad applications that extend beyond any single type of spectroscopy or system.
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Affiliation(s)
- Daniel Konstantinovsky
- Department of Chemistry, Yale University, New Haven, CT, USA 06511
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA 06511
| | - Elsa C. Y. Yan
- Department of Chemistry, Yale University, New Haven, CT, USA 06511
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Yale University, New Haven, CT, USA 06511
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA 06511
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8
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Krekic S, Mero M, Kuhl M, Balasubramanian K, Dér A, Heiner Z. Photoactive Yellow Protein Adsorption at Hydrated Polyethyleneimine and Poly-l-Glutamic Acid Interfaces. Molecules 2023; 28:molecules28104077. [PMID: 37241818 DOI: 10.3390/molecules28104077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/07/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Chiral and achiral vibrational sum-frequency generation (VSFG) spectroscopy was performed in the 1400-1700 and 2800-3800 cm-1 range to study the interfacial structure of photoactive yellow protein (PYP) adsorbed on polyethyleneimine (PEI) and poly-l-glutamic acid (PGA) surfaces. Nanometer-thick polyelectrolyte layers served as the substrate for PYP adsorption, with 6.5-pair layers providing the most homogeneous surfaces. When the topmost material was PGA, it acquired a random coil structure with a small number of β2-fibrils. Upon adsorption on oppositely charged surfaces, PYP yielded similar achiral spectra. However, the VSFG signal intensity increased for PGA surfaces with a concomitant redshift of the chiral Cα-H and N-H stretching bands, suggesting increased adsorption for PGA compared to PEI. At low wavenumbers, both the backbone and the side chains of PYP induced drastic changes to all measured chiral and achiral VSFG spectra. Decreasing ambient humidity led to the loss of tertiary structure with a re-orientation of α-helixes, evidenced by a strongly blue-shifted chiral amide I band of the β-sheet structure with a shoulder at 1654 cm-1. Our observations indicate that chiral VSFG spectroscopy is not only capable of determining the main type of secondary structure of PYP, i.e., β-scaffold, but is also sensitive to tertiary protein structure.
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Affiliation(s)
- Szilvia Krekic
- School of Analytical Sciences Adlershof, Humboldt-Universität zu Berlin, 12489 Berlin, Germany
- Institute of Biophysics, Biological Research Centre, 6726 Szeged, Hungary
- Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, 6720 Szeged, Hungary
| | - Mark Mero
- Max Born Institute for Nonlinear Optics and Short Pulse Spectroscopy, 12489 Berlin, Germany
| | - Michel Kuhl
- School of Analytical Sciences Adlershof, Humboldt-Universität zu Berlin, 12489 Berlin, Germany
- Department of Chemistry and IRIS Adlershof, Humboldt-Universität zu Berlin, 12489 Berlin, Germany
| | - Kannan Balasubramanian
- School of Analytical Sciences Adlershof, Humboldt-Universität zu Berlin, 12489 Berlin, Germany
- Department of Chemistry and IRIS Adlershof, Humboldt-Universität zu Berlin, 12489 Berlin, Germany
| | - András Dér
- Institute of Biophysics, Biological Research Centre, 6726 Szeged, Hungary
| | - Zsuzsanna Heiner
- School of Analytical Sciences Adlershof, Humboldt-Universität zu Berlin, 12489 Berlin, Germany
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9
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Konstantinovsky D, Perets EA, Santiago T, Olesen K, Wang Z, Soudackov AV, Yan ECY, Hammes-Schiffer S. Design of an Electrostatic Frequency Map for the NH Stretch of the Protein Backbone and Application to Chiral Sum Frequency Generation Spectroscopy. J Phys Chem B 2023; 127:2418-2429. [PMID: 36916645 PMCID: PMC10409516 DOI: 10.1021/acs.jpcb.3c00217] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
We develop an electrostatic map for the vibrational NH stretch (amide A) of the protein backbone with a focus on vibrational chiral sum frequency generation spectroscopy (chiral SFG). Chiral SFG has been used to characterize protein secondary structure at interfaces using the NH stretch and to investigate chiral water superstructures around proteins using the OH stretch. Interpretation of spectra has been complicated because the NH stretch and OH stretch overlap spectrally. Although an electrostatic map for water OH developed by Skinner and co-workers was used previously to calculate the chiral SFG response of water structures around proteins, a map for protein NH that is directly responsive to biological complexity has yet to be developed. Here, we develop such a map, linking the local electric field to vibrational frequencies and transition dipoles. We apply the map to two protein systems and achieve much better agreement with experiment than was possible in our previous studies. We show that couplings between NH and OH vibrations are crucial to the line shape, which informs the interpretation of chiral SFG spectra, and that the chiral NH stretch response is sensitive to small differences in structure. This work increases the utility of the NH stretch in biomolecular spectroscopy.
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Affiliation(s)
- Daniel Konstantinovsky
- Department of Chemistry, Yale University, New Haven, CT 06520, United States
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, United States
| | - Ethan A. Perets
- Department of Chemistry, Yale University, New Haven, CT 06520, United States
- Current Address: Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, United States
| | - Ty Santiago
- Department of Chemistry, Yale University, New Haven, CT 06520, United States
| | - Kristian Olesen
- Department of Chemistry, Yale University, New Haven, CT 06520, United States
| | - Zhijie Wang
- Department of Chemistry, Yale University, New Haven, CT 06520, United States
| | | | - Elsa C. Y. Yan
- Department of Chemistry, Yale University, New Haven, CT 06520, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Yale University, New Haven, CT 06520, United States
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, United States
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10
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Konstantinovsky D, Perets EA, Santiago T, Velarde L, Hammes-Schiffer S, Yan ECY. Detecting the First Hydration Shell Structure around Biomolecules at Interfaces. ACS CENTRAL SCIENCE 2022; 8:1404-1414. [PMID: 36313165 PMCID: PMC9615115 DOI: 10.1021/acscentsci.2c00702] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Indexed: 05/15/2023]
Abstract
Understanding the role of water in biological processes remains a central challenge in the life sciences. Water structures in hydration shells of biomolecules are difficult to study in situ due to overwhelming background from aqueous environments. Biological interfaces introduce additional complexity because biomolecular hydration differs at interfaces compared to bulk solution. Here, we perform experimental and computational studies of chiral sum frequency generation (chiral SFG) spectroscopy to probe chirality transfer from a protein to the surrounding water molecules. This work reveals that chiral SFG probes the first hydration shell around the protein almost exclusively. We explain the selectivity to the first hydration shell in terms of the asymmetry induced by the protein structure and specific protein-water hydrogen-bonding interactions. This work establishes chiral SFG as a powerful technique for studying hydration shell structures around biomolecules at interfaces, presenting new possibilities to address grand research challenges in biology, including the molecular origins of life.
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Affiliation(s)
- Daniel Konstantinovsky
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Department
of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Ethan A. Perets
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Ty Santiago
- Department
of Chemistry, University at Buffalo, Buffalo, New York 14260, United States
| | - Luis Velarde
- Department
of Chemistry, University at Buffalo, Buffalo, New York 14260, United States
| | | | - Elsa C. Y. Yan
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520, United States
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11
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Perets EA, Olesen KB, Yan ECY. Chiral Sum Frequency Generation Spectroscopy Detects Double-Helix DNA at Interfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:5765-5778. [PMID: 35482888 DOI: 10.1021/acs.langmuir.2c00365] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Many DNA-based technologies involve the immobilization of DNA and therefore require a fundamental understanding of the DNA structure-function relationship at interfaces. We present three immobilization methods compatible with chiral sum frequency generation (SFG) spectroscopy at interfaces. They are the "anchor" method for covalently attaching DNA on a glass surface, the "island" method for dropcasting DNA on solid substrates, and the "buoy" method using a hydrocarbon moiety for localizing DNA at the air-water interface. Although SFG was previously used to probe DNA, the chiral and achiral SFG responses of single-stranded and double-stranded DNA have not been compared systemically. Using the three immobilization methods, we obtain the achiral and chiral C-H stretching spectra. The results introduce four potential applications of chiral SFG. First, chiral SFG gives null response from single-stranded DNA but prominent signals from double-stranded DNA, providing a simple binary readout for label-free detection of DNA hybridization. Second, with heterodyne detection, chiral SFG gives an opposite-signed spectral response useful for distinguishing native (D-) right-handed double helix from non-native (L-) left-handed double helix. Third, chiral SFG captures the aromatic C-H stretching modes of nucleobases that emerge upon hybridization, revealing the power of chiral SFG to probe highly localized molecular structures within DNA. Finally, chiral SFG is sensitive to macroscopic chirality but not local chiral centers and thus can detect not only canonical antiparallel double helix but also other DNA secondary structures, such as a poly-adenine parallel double helix. Our work benchmarks the SFG responses of DNA immobilized by the three distinct methods, building a basis for new chiral SFG applications to solve fundamental and biotechnological problems.
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Affiliation(s)
- Ethan A Perets
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Kristian B Olesen
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Elsa C Y Yan
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
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12
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Blackburn TJ, Tyler SM, Pemberton JE. Optical Spectroscopy of Surfaces, Interfaces, and Thin Films. Anal Chem 2022; 94:515-558. [DOI: 10.1021/acs.analchem.1c05323] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Thomas J. Blackburn
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States
| | - Sarah M. Tyler
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States
| | - Jeanne E. Pemberton
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States
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13
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Konstantinovsky D, Perets EA, Yan ECY, Hammes-Schiffer S. Simulation of the Chiral Sum Frequency Generation Response of Supramolecular Structures Requires Vibrational Couplings. J Phys Chem B 2021; 125:12072-12081. [PMID: 34699209 PMCID: PMC9059521 DOI: 10.1021/acs.jpcb.1c06360] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chiral vibrational sum frequency generation (SFG) spectroscopy probes the structure of the solvation shell around chiral macromolecules. The dominant theoretical framework for understanding the origin of chiral SFG signals is based on the analysis of molecular symmetry, which assumes no interaction between molecules. However, water contains strong intermolecular interactions that significantly affect its properties. Here, the role of intermolecular vibrational coupling in the chiral SFG response of the O-H stretch of water surrounding an antiparallel β-sheet at the vacuum-water interface is investigated. Both intramolecular and intermolecular couplings between O-H groups are required to simulate the full lineshape of the chiral SFG signal. This dependence is also observed for a chiral water dimer, illustrating that this phenomenon is not specific to larger systems. We also find that a dimer of C3v molecules predicted to be chirally SFG-inactive by the symmetry-based theory can generate a chiral SFG signal when intermolecular couplings are considered, suggesting that even highly symmetric solvent molecules may produce chiral SFG signals when interacting with a chiral solute. The consideration of intermolecular couplings extends the prevailing theory of the chiral SFG response to structures larger than individual molecules and provides guidelines for future modeling.
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Affiliation(s)
- Daniel Konstantinovsky
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Ethan A. Perets
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - E. Chui-Ying Yan
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
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14
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Javanshad R, Venter AR. Effects of amino acid additives on protein solubility - insights from desorption and direct electrospray ionization mass spectrometry. Analyst 2021; 146:6592-6604. [PMID: 34586125 DOI: 10.1039/d1an01392k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Naturally occurring amino acids have been broadly used as additives to improve protein solubility and inhibit aggregation. In this study, improvements in protein signal intensity obtained with the addition of L-serine, and structural analogs, to the desorption electrospray ionization mass spectrometry (DESI-MS) spray solvent were measured. The results were interpreted at the hand of proposed mechanisms of solution additive effects on protein solubility and dissolution. DESI-MS allows for these processes to be studied efficiently using dilute concentrations of additives and small amounts of proteins, advantages that represent real benefits compared to classical methods of studying protein stability and aggregation. We show that serine significantly increases the protein signal in DESI-MS when native proteins are undergoing unfolding during the dissolution process with an acidic solvent system (p-value = 0.0001), or with ammonium bicarbonate under denaturing conditions for proteins with high isoelectric points (p-value = 0.001). We establish that a similar increase in the protein signal cannot be observed with direct ESI-MS, and the observed increase is therefore not related to ionization processes or changes in the physical properties of the bulk solution. The importance of the presence of serine during protein conformational changes while undergoing dissolution is demonstrated through comparisons between the analyses of proteins deposited in native or unfolded states and by using native state-preserving and denaturing desorption solvents. We hypothesize that direct, non-covalent interactions involving all three functional groups of serine are involved in the beneficial effect on protein solubility and dissolution. Supporting evidence for a direct interaction include a reduction in efficacy with D-serine or the racemic mixture, indicating a non-bulk-solution physical property effect; insensitivity to the sample surface type or relative placement of serine addition; and a reduction in efficacy with any modifications to the serine structure, most notably the carboxyl functional group. An alternative hypothesis, also supported by some of our observations, could involve the role of serine clusters in the mechanism of solubility enhancement. Our study demonstrates the capability of DESI-MS together with complementary ESI-MS experiments as a novel tool for understanding protein solubility and dissolution and investigating the mechanism of action for solubility-enhancing additives.
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Affiliation(s)
- Roshan Javanshad
- Department of Chemistry, Western Michigan University, Kalamazoo, MI 49008-5413, USA.
| | - Andre R Venter
- Department of Chemistry, Western Michigan University, Kalamazoo, MI 49008-5413, USA.
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15
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Carpenter AP, Christoffersen EL, Mapile AN, Richmond GL. Assessing the Impact of Solvent Selection on Vibrational Sum-Frequency Scattering Spectroscopy Experiments. J Phys Chem B 2021; 125:3216-3229. [PMID: 33739105 DOI: 10.1021/acs.jpcb.1c00188] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The development of vibrational sum-frequency scattering (S-VSF) spectroscopy has opened the door to directly probing nanoparticle surfaces with an interfacial and chemical specificity that was previously reserved for planar interfacial systems. Despite its potential, challenges remain in the application of S-VSF spectroscopy beyond simplified chemical systems. One such challenge includes infrared absorption by an absorptive continuous phase, which will alter the spectral lineshapes within S-VSF spectra. In this study, we investigate how solvent vibrational modes manifest in S-VSF spectra of surfactant stabilized nanoemulsions and demonstrate how corrections for infrared absorption can recover the spectral features of interfacial solvent molecules. We also investigate infrared absorption for systems with the absorptive phase dispersed in a nonabsorptive continuous phase to show that infrared absorption, while reduced, will still impact the S-VSF spectra. These studies are then used to provide practical recommendations for anyone wishing to use S-VSF to study nanoparticle surfaces where absorptive solvents are present.
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Affiliation(s)
- Andrew P Carpenter
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97405, United States
| | - Evan L Christoffersen
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97405, United States
| | - Ashley N Mapile
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97405, United States
| | - Geraldine L Richmond
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97405, United States
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16
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Windowless detection geometry for sum frequency scattering spectroscopy in the C-D and amide I regions. Biointerphases 2021; 16:011201. [PMID: 33706523 DOI: 10.1116/6.0000419] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Understanding the structure and chemistry of nanoscopic surfaces is an important challenge for biointerface sciences. Sum frequency scattering (SFS) spectroscopy can specifically probe the surfaces of nanoparticles, vesicles, liposomes, and other materials relevant to biomaterial research, and, as a vibrational spectroscopy method, it can provide molecular level information about the surface chemistry. SFS is particularly promising to probe the structure of proteins, and other biological molecules, at nanoparticle surfaces. Here, amide I spectra can provide information about protein folding and orientation, while spectra in the C-D and C-H stretching regions allow experiments to determine the mode of interaction between particle surfaces and proteins. Methods used currently employ a closed liquid cell or cuvette, which works extremely well for C-H and phosphate regions but is often impeded in the amide I and C-D regions by a strong background signal that originates from the window material of the sample cells. Here, we discuss a windowless geometry for collecting background-free and high-fidelity SFS spectra in the amide I and C-D regions. We demonstrate the improvement in spectra quality by comparing SFS spectra of unextruded, multilamellar vesicles in a sample cuvette with those recorded using the windowless geometry. The sample geometry we propose will enable new experiments using SFS as a probe for protein-particle interactions.
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17
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Hazam PK, Phukan C, Akhil R, Singh A, Ramakrishnan V. Antimicrobial effects of syndiotactic polypeptides. Sci Rep 2021; 11:1823. [PMID: 33469079 PMCID: PMC7815786 DOI: 10.1038/s41598-021-81394-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 12/21/2020] [Indexed: 12/03/2022] Open
Abstract
We present design and antibacterial studies of stereochemically diversified antimicrobial peptides against multidrug-resistant bacterial pathogens. Syndiotactic polypeptides are polymers of alternating L and D amino acids with LDLD or DLDL backbone stereochemical sequence, which can form stable gramicidin like helical conformations. We designed, synthesized and characterized eight model molecular systems with varied electrostatic fingerprints, modulated through calibrated sequence positioning. Six out of eight model systems showed very impressive antimicrobial activity against three difficult to treat bacterial species, Gentamicin resistant MRSA, E. coli and Mycobacterium. More importantly, the designed LDLD peptides were equally potent in serum, an important drawback of poly L peptide sequences due to enzyme mediated degradation and ion sensitivity. Further, we tested the activity of the designed peptides against drug-resistant clinical isolates of Staphylococcus aureus and Escherichia coli. Molecular dynamics simulation studies suggest formation of an assembly of individual peptides, preceding the membrane interaction and deformation. The activity estimates are comparable with the available peptide based antimicrobials, and are also highly specific and less toxic as per standard estimates. Incorporation of D amino-acids can significantly expand the peptide design space, which can in turn manifest in future biomaterial designs, especially antimicrobials.
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Affiliation(s)
- Prakash Kishore Hazam
- Molecular Informatics and Design Laboratory, Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.,Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research Guwahati, Guwahati, Assam, 781125, India
| | - Chimanjita Phukan
- Guwahati Medical College Hospital, Bhangagarh, Guwahati, Assam, 781032, India
| | - R Akhil
- Molecular Informatics and Design Laboratory, Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Anjali Singh
- Molecular Informatics and Design Laboratory, Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Vibin Ramakrishnan
- Molecular Informatics and Design Laboratory, Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.
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18
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Mirror-image antiparallel β-sheets organize water molecules into superstructures of opposite chirality. Proc Natl Acad Sci U S A 2020; 117:32902-32909. [PMID: 33318168 DOI: 10.1073/pnas.2015567117] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Biomolecular hydration is fundamental to biological functions. Using phase-resolved chiral sum-frequency generation spectroscopy (SFG), we probe molecular architectures and interactions of water molecules around a self-assembling antiparallel β-sheet protein. We find that the phase of the chiroptical response from the O-H stretching vibrational modes of water flips with the absolute chirality of the (l-) or (d-) antiparallel β-sheet. Therefore, we can conclude that the (d-) antiparallel β-sheet organizes water solvent into a chiral supermolecular structure with opposite handedness relative to that of the (l-) antiparallel β-sheet. We use molecular dynamics to characterize the chiral water superstructure at atomic resolution. The results show that the macroscopic chirality of antiparallel β-sheets breaks the symmetry of assemblies of surrounding water molecules. We also calculate the chiral SFG response of water surrounding (l-) and (d-) LK7β to confirm the presence of chiral water structures. Our results offer a different perspective as well as introduce experimental and computational methodologies for elucidating hydration of biomacromolecules. The findings imply potentially important but largely unexplored roles of water solvent in chiral selectivity of biomolecular interactions and the molecular origins of homochirality in the biological world.
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19
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Hu XH, Fu L, Hou J, Zhang YN, Zhang Z, Wang HF. N-H Chirality in Folded Peptide LK 7β Is Governed by the C α-H Chirality. J Phys Chem Lett 2020; 11:1282-1290. [PMID: 31977221 DOI: 10.1021/acs.jpclett.9b03470] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Recent chiral sum-frequency generation vibrational spectroscopy (SFG-VS) measurements revealed that two N-H stretching modes in the 3100-3500 cm-1 range in folded peptide LK7β exhibit chiral characteristics. Here, we report the first phase-resolved subwavenumber high-resolution broadband SFG-VS (HR-BB-SFG-VS) measurement of the folded peptide LK7β. The results show that this chiral N-H band consists of four, instead of two, distinctive peaks, and they are with two groups of opposite spectral phases. Moreover, the phases of these N-H peaks completely flip from the l-LK7β to the d-LK7β peptide, suggesting that the chirality of the N-H in the folded peptide LK7β is completely governed by the chirality of the Cα-H of the amino acids. This discovery provides a clue on why proteins in nature are composed of the α-amino acids rather than β- or γ-amino acids and may help us understand how life works.
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Affiliation(s)
- Xiao-Hua Hu
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials , Fudan University , 220 Handan Road , Shanghai 200433 , China
| | - Li Fu
- William R. Wiley Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Jian Hou
- Beijing National Laboratory for Molecular Sciences , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , China
| | - Yue-Ning Zhang
- Beijing National Laboratory for Molecular Sciences , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , China
| | - Zhen Zhang
- Beijing National Laboratory for Molecular Sciences , Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190 , China
| | - Hong-Fei Wang
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials , Fudan University , 220 Handan Road , Shanghai 200433 , China
- School of Science , Westlake University , 18 Shilongshan Road , Hangzhou 310024 , China
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20
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Zhang J, Tan J, Pei R, Ye S. Acidic Environment Significantly Alters Aggregation Pathway of Human Islet Amyloid Polypeptide at Negative Lipid Membrane. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:1530-1537. [PMID: 31995712 DOI: 10.1021/acs.langmuir.9b03623] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The misfolding and aggregation of human islet amyloid polypeptide (hIAPP) at cell membrane has a close relationship with the development of type 2 diabetes (T2DM). This aggregation process is susceptible to various physiologically related factors, and systematic studies on condition-mediated hIAPP aggregation are therefore essential for a thorough understanding of the pathology of T2DM. In this study, we combined surface-sensitive amide I and amide II spectral signals from the protein backbone, generated simultaneously in a highly sensitive femtosecond broad-band sum frequency generation vibrational spectroscopy system, to examine the effect of environmental pH on the dynamical structural changes of hIAPP at membrane surface in situ and in real time. Such a combination can directly discriminate the formation of β-hairpin-like monomer and oligomer/fibril at the membrane surface. It is evident that, in an acidic milieu, hIAPP slows down its conformational evolution and alters its aggregation pathway, leading to the formation of off-pathway oligomers. When matured hIAPP aggregates are exposed to basic subphase, partial conversion from β-sheet oligomers into ordered β-sheet fibrillar structures is observed. When exposed to acidic environment, however, hIAPP fibrils partially converse into more loosely patterned β-sheet oligomeric structures.
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Affiliation(s)
- Jiahui Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, and Department of Chemical Physics , University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Junjun Tan
- Hefei National Laboratory for Physical Sciences at the Microscale, and Department of Chemical Physics , University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Ruoqi Pei
- Hefei National Laboratory for Physical Sciences at the Microscale, and Department of Chemical Physics , University of Science and Technology of China , Hefei , Anhui 230026 , China
| | - Shuji Ye
- Hefei National Laboratory for Physical Sciences at the Microscale, and Department of Chemical Physics , University of Science and Technology of China , Hefei , Anhui 230026 , China
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21
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Hosseinpour S, Roeters SJ, Bonn M, Peukert W, Woutersen S, Weidner T. Structure and Dynamics of Interfacial Peptides and Proteins from Vibrational Sum-Frequency Generation Spectroscopy. Chem Rev 2020; 120:3420-3465. [DOI: 10.1021/acs.chemrev.9b00410] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Saman Hosseinpour
- Institute of Particle Technology (LFG), Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
| | | | - Mischa Bonn
- Molecular Spectroscopy Department, Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Wolfgang Peukert
- Institute of Particle Technology (LFG), Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
| | - Sander Woutersen
- Van’t Hoff Institute for Molecular Sciences, University of Amsterdam, 1098 EP Amsterdam, The Netherlands
| | - Tobias Weidner
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
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