1
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Clever C, Wierzbinski E, Bloom BP, Lu Y, Grimm HM, Rao SR, Horne WS, Waldeck DH. Benchmarking Chiral Induced Spin Selectivity Measurements ‐ Towards Meaningful Comparisons of Chiral Biomolecule Spin Polarizations. Isr J Chem 2022. [DOI: 10.1002/ijch.202200045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Caleb Clever
- Department of Chemistry University of Pittsburgh Pittsburgh PA 15260 USA
| | - Emil Wierzbinski
- Department of Chemistry University of Pittsburgh Pittsburgh PA 15260 USA
| | - Brian P. Bloom
- Department of Chemistry University of Pittsburgh Pittsburgh PA 15260 USA
| | - Yiyang Lu
- Department of Chemistry University of Pittsburgh Pittsburgh PA 15260 USA
| | - Haley M. Grimm
- Department of Chemistry University of Pittsburgh Pittsburgh PA 15260 USA
| | - Silpa R. Rao
- Department of Chemistry University of Pittsburgh Pittsburgh PA 15260 USA
| | - W. Seth Horne
- Department of Chemistry University of Pittsburgh Pittsburgh PA 15260 USA
| | - David H. Waldeck
- Department of Chemistry University of Pittsburgh Pittsburgh PA 15260 USA
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2
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Ghosh S, Tran PN, McElheny D, Perez JJ, Nguyen AI. Peptidic Scaffolds Enable Rapid and Multivariate Secondary Sphere Evolution for an Abiotic Metallocatalyst. Inorg Chem 2022; 61:6679-6687. [PMID: 35446044 DOI: 10.1021/acs.inorgchem.2c00901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metalloenzymes have benefited from the iterative process of evolution to achieve the precise arrangements of secondary sphere non-covalent interactions that enhance metal-centered catalysis. Iterative synthesis of scaffolds that display complex secondary sphere elements in abiotic systems can be highly challenging and time-intensive. To overcome this synthetic bottleneck, we developed a highly modular and rapid synthetic strategy, leveraging the efficiency of solid-phase peptide synthesis and conformational control afforded by non-canonical residues to construct a ligand platform displaying up to four unique residues of varying electronics and sterics in the secondary coordination sphere. As a proof-of-concept that peptidic secondary sphere can cooperate with the metal complex, we applied this scaffold to a well-known, modestly active C-H oxidizing Fe catalyst to evolve specific non-covalent interactions that is more than double its catalytic activity. Solution-state NMR structures of several catalyst variants suggest that higher activity is correlated with a hydrophobic pocket above the Fe center that may enhance the formation of a catalyst-substrate complex. Above all, we show that peptides are a convenient, highly modular, and structurally defined ligand platform for creating secondary coordination spheres that comprise multiple, diverse functional groups.
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Affiliation(s)
- Sabari Ghosh
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Phuong Nguyen Tran
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Dan McElheny
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Juan J Perez
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Andy I Nguyen
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois 60607, United States
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3
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Banerjee R, Sheet T, Banerjee S, Biondi B, Formaggio F, Toniolo C, Peggion C. C α-Methyl-l-valine: A Preferential Choice over α-Aminoisobutyric Acid for Designing Right-Handed α-Helical Scaffolds. Biochemistry 2021; 60:2704-2714. [PMID: 34463474 DOI: 10.1021/acs.biochem.1c00340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In synthetic peptides containing Gly and coded α-amino acids, one of the most common practices to enhance their helical extent is to incorporate a large number of l-Ala residues along with noncoded, strongly foldameric α-aminoisobutyric acid (Aib) units. Earlier studies have established that Aib-based peptides, with propensity for both the 310- and α-helices, have a tendency to form ordered three-dimensional structure that is much stronger than that exhibited by their l-Ala rich counterparts. However, the achiral nature of Aib induces an inherent, equal preference for the right- and left-handed helical conformations as found in Aib homopeptide stretches. This property poses challenges in the analysis of a model peptide helical conformation based on chirospectroscopic techniques like electronic circular dichroism (ECD), a very important tool for assigning secondary structures. To overcome such ambiguity, we have synthesized and investigated a thermally stable 14-mer peptide in which each of the Aib residues of our previously designed and reported analogue ABGY (where B stands for Aib) is replaced by Cα-methyl-l-valine (L-AMV). Analysis of the results described here from complementary ECD and 1H nuclear magnetic resonance spectroscopic techniques in a variety of environments firmly establishes that the L-AMV-containing peptide exhibits a significantly stronger preference compared to that of its Aib parent in terms of conferring α-helical character. Furthermore, being a chiral α-amino acid, L-AMV shows an intrinsic, extremely strong bias for a quite specific (right-handed) screw sense. These findings emphasize the relevance of L-AMV as a more appropriate unit for the design of right-handed α-helical peptide models that may be utilized as conformationally constrained scaffolds.
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Affiliation(s)
| | | | | | - Barbara Biondi
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy.,Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
| | - Fernando Formaggio
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy.,Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
| | - Claudio Toniolo
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy.,Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
| | - Cristina Peggion
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy.,Institute of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
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4
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Pal D, Sahu S, Banerjee R. New facets of larger Nest motifs in proteins. Proteins 2020; 88:1413-1422. [PMID: 32519388 DOI: 10.1002/prot.25961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 06/06/2020] [Indexed: 11/07/2022]
Abstract
The Nest is a concave-shaped structural motif in proteins formed by consecutive enantiomeric left-handed (L) and right-handed (R) helical conformation of the backbone. This important motif subsumes many turn and helix capping structures and binds electron-rich ligands. Simple Nests are either RL or LR. Larger Nests (>2 residues long) may be RLR, LRL, RLRL, and so forth, being considered as composed of overlapping simple Nests. The larger Nests remain under-explored despite their widely known contributions to protein function. In our study, we address whether the recurrence of enantiomeric geometry in the larger Nests constrains the peptide backbone such that distinct compositional and conformational preferences are seen compared to simple Nests. Our analysis reveals the critical role of the L helical torsion angle in the formation of larger Nests. This can be observed through the higher propensity of residue or secondary structure combinations in LR and LRL backbone conformation in comparison to RL or RLR, although LR/LRL is considerably lower by occurrence. We also find that the most abundant doublets and triplets in Nests have a propensity for particular secondary structures, suggesting a strong sequence-structure relationship in the larger Nest. Overall, our analysis corroborates distinct features of simple and the larger Nests. Such insights would be helpful towards in-vitro design of peptides and peptidomimetic studies.
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Affiliation(s)
- Debnath Pal
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Subhankar Sahu
- Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, Kolkata, West Bengal, India
| | - Raja Banerjee
- Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, Kolkata, West Bengal, India.,Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, Kolkata, West Bengal, India
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5
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Sheet T, Banerjee R. Design of a Peptide-Based Model Leads for Scavenging Anions. ACS OMEGA 2020; 5:9759-9767. [PMID: 32391463 PMCID: PMC7203709 DOI: 10.1021/acsomega.9b04180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 04/03/2020] [Indexed: 06/11/2023]
Abstract
Among several peptide-based anion recognition motifs, the "CαNN" motif containing C-1 α, N0, and N+1 of three consecutive residues is unique in its mode of interaction. Having a spatial geometry of βαα or βαβ, this motif occurs in the N terminus of a helix and often found at the functional interface of a protein, mediating crucial biological significance upon interaction with anion(s). The interaction of anion(s) with chimeric peptide sequences containing the naturally occurring "CαNN" motif (CPS224Ac, CPS226, and CPS228) reported in our previous attempts strongly confirms that the information regarding the interaction is embedded within the local sequences of the motif segment. At these prevailing circumstances, an effort has been pursued to design novel scaffolds based on the "CαNN" motif for achieving better recognition of anion(s). Exploring the existing data set of the "CαNN" motif available in the FSSP database, four novel peptide-based scaffolds have been designed (DS1, DS2, DS3, and DS4), and preliminary screenings have been performed using computational approaches. Our initial work suggests that two (DS1 and DS3) out of the four scaffolds are potential candidates for better anion recognition. By employing biophysical characterization using both qualitative and quantitative measures, in this present study, we report the interaction of sulfate and phosphate ions with these two designed scaffolds, in which there is much better recognition of anions by these scaffolds than the natural sequences, justifying their logical engineering. Our observation strongly suggests that these designed scaffolds are better potential candidates than those of the naturally occurring "CαNN" motif in terms of anion recognition and could be utilized for the scavenging of anion(s) for different purposes.
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Affiliation(s)
- Tridip Sheet
- Department
of Bioinformatics, Maulana Abul Kalam Azad
University of Technology, West Bengal (Formerly Known as West Bengal
University of Technology), BF-142, Sector-1, Salt Lake, Kolkata 700064, India
| | - Raja Banerjee
- Department
of Bioinformatics, Maulana Abul Kalam Azad
University of Technology, West Bengal (Formerly Known as West Bengal
University of Technology), BF-142, Sector-1, Salt Lake, Kolkata 700064, India
- Department
of Biotechnology, Maulana Abul Kalam Azad
University of Technology, West Bengal (Formerly Known as West Bengal
University of Technology), BF-142, Sector-1, Salt Lake, Kolkata 700064, India
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6
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Lübtow MM, Haider MS, Kirsch M, Klisch S, Luxenhofer R. Like Dissolves Like? A Comprehensive Evaluation of Partial Solubility Parameters to Predict Polymer-Drug Compatibility in Ultrahigh Drug-Loaded Polymer Micelles. Biomacromolecules 2019; 20:3041-3056. [PMID: 31318531 DOI: 10.1021/acs.biomac.9b00618] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Despite decades of research, our understanding of the molecular interactions between drugs and polymers in drug-loaded polymer micelles does not extend much beyond concepts such as "like-dissolves-like" or hydrophilic/hydrophobic. However, polymer-drug compatibility strongly affects formulation properties and therefore the translation of a formulation into the clinics. Specific interactions such as hydrogen-bonding, π-π stacking, or coordination interactions can be utilized to increase drug loading. This is commonly based on trial and error and eventually leads to an optimized drug carrier. Unfortunately, due to the unique characteristics of each drug, the deduction of advanced general concepts remains challenging. Furthermore, the introduction of complex moieties or specifically modified polymers hampers systematic investigations regarding polymer-drug compatibility as well as clinical translation. In this study, we reduced the complexity to isolate the crucial factors determining drug loading. Therefore, the compatibility of 18 different amphiphilic polymers for five different hydrophobic drugs was determined empirically. Subsequently, the obtained specificities were compared to theoretical compatibilities derived from either the Flory-Huggins interaction parameters or the Hansen solubility parameters. In general, the Flory-Huggins interaction parameters were less suited to correctly estimate the experimental drug solubilization compared to the Hansen solubility parameters. The latter were able to correctly predict some trend regarding good and poor solubilizers, yet the overall predictive strength of Hansen solubility parameters is clearly unsatisfactory.
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Affiliation(s)
- Michael M Lübtow
- Functional Polymer Materials, Chair for Advanced Materials Synthesis, Department of Chemistry and Pharmacy and Bavarian Polymer Institute , University of Würzburg , Röntgenring 11 , 97070 Würzburg , Germany
| | - Malik Salman Haider
- Functional Polymer Materials, Chair for Advanced Materials Synthesis, Department of Chemistry and Pharmacy and Bavarian Polymer Institute , University of Würzburg , Röntgenring 11 , 97070 Würzburg , Germany
| | - Marius Kirsch
- Functional Polymer Materials, Chair for Advanced Materials Synthesis, Department of Chemistry and Pharmacy and Bavarian Polymer Institute , University of Würzburg , Röntgenring 11 , 97070 Würzburg , Germany
| | - Stefanie Klisch
- Functional Polymer Materials, Chair for Advanced Materials Synthesis, Department of Chemistry and Pharmacy and Bavarian Polymer Institute , University of Würzburg , Röntgenring 11 , 97070 Würzburg , Germany
| | - Robert Luxenhofer
- Functional Polymer Materials, Chair for Advanced Materials Synthesis, Department of Chemistry and Pharmacy and Bavarian Polymer Institute , University of Würzburg , Röntgenring 11 , 97070 Würzburg , Germany
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7
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Sahu S, Sheet T, Banerjee R. Interaction landscape of a 'C αNN' motif with arsenate and arsenite: a potential peptide-based scavenger of arsenic. RSC Adv 2019; 9:1062-1074. [PMID: 35517606 PMCID: PMC9059529 DOI: 10.1039/c8ra08225a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 12/08/2018] [Indexed: 12/01/2022] Open
Abstract
Arsenic (As) is a toxic metalloid that has drawn immense attention from the scientific community recently due to its fatal effects through its unwanted occurrence in ground water around the globe. The presence of an excess amount of water soluble arsenate and/or arsenite salt (permissible limit 10 μg L-1 as recommended by the WHO) in water has been correlated with several human diseases. Although arsenate (HAsO4 2-) is a molecular analogue of phosphate (HPO4 2-), phosphate is indispensable for life, while arsenic and its salts are toxic. Therefore, it is worthwhile to focus on the removal of arsenic from water. Towards this end, the design of peptide-based scaffolds for the recognition of arsenate and arsenite would add a new dimension. Utilizing the stereochemical similarity between arsenate (HAsO4 2-) and phosphate (HPO4 2-), we successfully investigated the recognition of arsenate and arsenite with a naturally occurring novel phosphate binding 'CαNN' motif and its related designed analogues. Using computational as well as biophysical approaches, for the first time, we report here that a designed peptide-based scaffold based on the 'CαNN' motif can recognize anions of arsenic in a thermodynamically favorable manner in a context-free system. This peptide-based arsenic binding agent has the potential for future development as a scavenger of arsenic anions to obtain arsenic free water.
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Affiliation(s)
- Subhankar Sahu
- Department of Biotechnology and Head Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly Known as West Bengal University of Technology) BF-142, Salt Lake Kolkata 700064 West Bengal India
| | - Tridip Sheet
- Department of Biotechnology and Head Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly Known as West Bengal University of Technology) BF-142, Salt Lake Kolkata 700064 West Bengal India
| | - Raja Banerjee
- Department of Biotechnology and Head Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly Known as West Bengal University of Technology) BF-142, Salt Lake Kolkata 700064 West Bengal India
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8
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Grubišić S, Chandramouli B, Barone V, Brancato G. Chain length, temperature and solvent effects on the structural properties of α-aminoisobutyric acid homooligopeptides. Phys Chem Chem Phys 2018; 18:20389-98. [PMID: 27402118 DOI: 10.1039/c6cp01120a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Non-coded α-amino acids, originally exploited by nature, have been successfully reproduced by recent synthetic strategies to confer special structural and functional properties to small peptides. The most known and well-studied atypical residue is α-aminoisobutyric acid (Aib), which is contained in a fairly large number of peptides with known antibiotic effects. Here, we report on a molecular dynamics (MD) study of a series of homooligopeptides based on α-aminoisobutyric acid (Aib) with increasing length (Ac-(Aib)n-NMe, n = 5, 6, 7 and 10) and at various temperatures, employing a recent extension of the AMBER force field tailored for the Aib residue. Solvent effects have been analyzed by comparative MD simulations of a heptapeptide in water and dimethylsulfoxide at different temperatures. Our results show that the preference for the 310- and/or α-helix structures, which typically characterize Aib based peptides, is finely tuned by several factors including the chain length, temperature and solvent nature. While the transitions between intra-molecular i → i + 3 and i → i + 4 hydrogen bonds characterizing 310 and α-helices, respectively, are rather fast in small peptides (in the picosecond timescale), our analysis shows that the above physical and chemical factors modulate the relative equilibrium populations of the two helical structures. The obtained results nicely agree with available experimental data and support the use of the new force field for modeling Aib containing peptides.
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Affiliation(s)
- Sonja Grubišić
- Center for Chemistry, IHTM, University of Belgrade, Njegoševa 12, P.O. Box 815, 11001 Belgrade, Serbia.
| | - Balasubramanian Chandramouli
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy. and Istituto Nazionale di Fisica Nucleare, Largo Pontecorvo 3, I-56100 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy. and Istituto Nazionale di Fisica Nucleare, Largo Pontecorvo 3, I-56100 Pisa, Italy
| | - Giuseppe Brancato
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy. and Istituto Nazionale di Fisica Nucleare, Largo Pontecorvo 3, I-56100 Pisa, Italy
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9
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Raggi L, Bada JL, Lazcano A. On the lack of evolutionary continuity between prebiotic peptides and extant enzymes. Phys Chem Chem Phys 2018; 18:20028-32. [PMID: 27121024 DOI: 10.1039/c6cp00793g] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The significance of experiments that claim to simulate the properties of prebiotic small peptides and polypeptides as models of the polymers that may have preceded proteins is critically addressed. As discussed here, most of these experiments are based only on a small number of a larger set of amino acids that may have been present in the prebiotic environment, supported by both experimental simulations and the repertoire of organic compounds reported in carbonaceous chondrites. Model experiments with small peptides may offer some insights into the processes that contributed to generate the chemical environment leading to the emergence of informational oligomers, but not to the origin of proteins. The large body of circumstantial evidence indicating that catalytic RNA played a key role in the origin of protein synthesis during the early stages of cellular evolution implies that the emergence of the genetic code and of protein biosynthesis are no longer synonymous with the origin of life. Hence, reports on the abiotic synthesis of small catalytic peptides under potential prebiotic conditions do not provide information on the origin of triplet encoded protein biosynthesis, but in some cases may serve as models to understand the properties of the earliest proteins.
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Affiliation(s)
- Luciana Raggi
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Apartado Postal 70-407, Cd. Universitaria, 04510 Ciudad de México, Mexico.
| | - Jeffrey L Bada
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA 92093-0212, USA
| | - Antonio Lazcano
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Apartado Postal 70-407, Cd. Universitaria, 04510 Ciudad de México, Mexico.
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10
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Marvin CW, Grimm HM, Miller NC, Horne WS, Hutchison GR. Interplay among Sequence, Folding Propensity, and Bio-Piezoelectric Response in Short Peptides and Peptoids. J Phys Chem B 2017; 121:10269-10275. [DOI: 10.1021/acs.jpcb.7b10085] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christopher W. Marvin
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Haley M. Grimm
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Nathaniel C. Miller
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - W. Seth Horne
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Geoffrey R. Hutchison
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
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11
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Structural Behavior of the Peptaibol Harzianin HK VI in a DMPC Bilayer: Insights from MD Simulations. Biophys J 2017. [PMID: 28636916 DOI: 10.1016/j.bpj.2017.05.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Microsecond molecular dynamics simulations of harzianin HK VI (HZ) interacting with a dimyristoylphosphatidylcholine bilayer were performed at the condition of low peptide-to-lipid ratio. Two orientations of HZ molecule in the bilayer were found and characterized. In the orientation perpendicular to the bilayer surface, HZ induces a local thinning of the bilayer. When inserted into the bilayer parallel to its surface, HZ is located nearly completely within the hydrophobic region of the bilayer. A combination of solid-state NMR and circular dichroism experiments found the latter orientation to be dominant. An extended sampling simulation provided qualitative results and showed the same orientation to be a global minimum of free energy. The secondary structure of HZ was characterized, and it was found to be located in the 310-helical family. The specific challenges of computer simulation of nonpolar peptides are discussed briefly.
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12
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Banerjee R, Sheet T. Ratio of ellipticities between 192 and 208 nm (R 1 ): An effective electronic circular dichroism parameter for characterization of the helical components of proteins and peptides. Proteins 2017; 85:1975-1982. [PMID: 28707342 DOI: 10.1002/prot.25351] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 07/09/2017] [Accepted: 07/10/2017] [Indexed: 01/28/2023]
Abstract
Circular dichroism (CD) spectroscopy represents an important tool for characterization of the peptide and protein secondary structures that mainly arise from the conformational disposition of the peptide backbone in solution. In 1991 Manning and Woody proposed that, in addition to the signal intensity, the ratio between [θ]nπ* and [θ]ππ*ǁ ((R2 ) ≅ [θ]222 /[θ]208 ), along with [θ]ππ*⊥ and [θ]ππ*ǁ ((R1 ) ≅ [θ]192 /[θ]208 ), may be utilized towards identifying the peptide/protein conformation (especially 310 - and α-helices). However, till date the use of the ratiometric ellipticity component for helical structure analysis of peptides and proteins has not been reported. We studied a series of temperature dependent CD spectra of a thermally stable, model helical peptide and its related analogs in water as a function of added 2,2,2-trifluoroethanol (TFE) in order to explore their landscape of helicity. For the first time, we have experimentally shown here that the R1 parameter can characterize better the individual helices, while the other parameter R2 and the signal intensity do not always converge. We emphasize the use of the R1 ratio of ellipticities for helical characterization because of the common origin of these two bands (exciton splitting of the amide π→ π* transition in a helical polypeptide). This approach may become worthwhile and timely with the increasing accessibility of CD synchrotron sources.
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Affiliation(s)
- Raja Banerjee
- Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly Known as West Bengal University of Technology), Salt Lake, Kolkata, 700064, West Bengal, India
| | - Tridip Sheet
- Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly Known as West Bengal University of Technology), Salt Lake, Kolkata, 700064, West Bengal, India
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13
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Sheet T, Ghosh S, Pal D, Banerjee R. Computational design of model scaffold for anion recognition based on the 'C α NN' motif. Biopolymers 2017; 108. [PMID: 27428807 DOI: 10.1002/bip.22921] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 07/05/2016] [Accepted: 07/14/2016] [Indexed: 11/06/2022]
Abstract
The 'novel phosphate binding 'Cα NN' motif', consisting of three consecutive amino acid residues, usually occurs in the protein loop regions preceding a helix. Recent computational and complementary biophysical experiments on a series of chimeric peptides containing the naturally occurring 'Cα NN' motif at the N-terminus of a designed helix establishes that the motif segment recognizes the anion (sulfate and phosphate ions) through local interaction along with extension of the helical conformation which is thermodynamically favored even in a context-free, nonproteinaceous isolated system. However, the strength of the interaction depends on the amino acid sequence/conformation of the motif. Such a locally-mediated recognition of anions validates its intrinsic affinity towards anions and confirms that the affinity for recognition of anions is embedded within the 'local sequence' of the motif. Based on the knowledge gathered on the sequence/structural aspects of the naturally occurring 'Cα NN' segment, which provides the guideline for rationally engineering model scaffolds, we have modeled a series of templates and investigated their interactions with anions using computational approach. Two of these designed scaffolds show more efficient anion recognition than those of the naturally occurring 'Cα NN' motif which have been studied. This may provide an avenue in designing better anion receptors suitable for various biochemical applications.
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Affiliation(s)
- Tridip Sheet
- Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly Known as West Bengal University of Technology), BF-142, Sector-1, Salt Lake, Kolkata, 700064, India
| | - Suvankar Ghosh
- Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly Known as West Bengal University of Technology), BF-142, Sector-1, Salt Lake, Kolkata, 700064, India
| | - Debnath Pal
- Indian Institute of Science, Bangalore, 560012, India
| | - Raja Banerjee
- Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly Known as West Bengal University of Technology), BF-142, Sector-1, Salt Lake, Kolkata, 700064, India
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14
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Dasgupta R, Ganguly HK, Modugula EK, Basu G. Type VIa β-turn-fused helix N-termini: A novel helix N-cap motif containing cis proline. Biopolymers 2016; 108. [PMID: 27428516 DOI: 10.1002/bip.22919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 07/07/2016] [Accepted: 07/14/2016] [Indexed: 11/05/2022]
Abstract
Helix N-capping motifs often form hydrogen bonds with terminal amide groups which otherwise would be free. Also, without an amide hydrogen, proline (trans) is over-represented at helix N-termini (N1 position) because this naturally removes the need to hydrogen bond one terminal amide. However, the preference of cisPro, vis-à-vis helix N-termini, is not known. We show that cisPro (αR or PPII ) often appears at the N-cap position (N0) of helices. The N-cap cisPro(αR ) is associated with a six-residue sequence motif - X(-2) -X(-1) -cisPro-X(1) -X(2) -X(3) - with preference for Glu/Gln at X(-1) , Phe/Tyr/Trp at X(1) and Ser/Thr at X(3) . The motif, formed by the fusion of a helix and a type VIa β-turn, contains a hydrogen bond between the side chain of X(-1) and the side chain/backbone of X(3) , a α-helical hydrogen bond between X(-2) and X(2) and stacking interaction between cisPro and an aromatic residue at X(1) . NMR experiments on peptides containing the motif and its variants showed that local interactions associated with the motif, as found in folded proteins, were not enough to significantly tilt the cis/trans equilibrium towards cisPro. This suggests that some other evolutionary pressure must select the cisPro motif (over transPro) at helix N-termini. Database analysis showed that >C = O of the pre-cisPro(αR ) residue at the helix N-cap, directed opposite to the N→C helical axis, participates in long-range interactions. We hypothesize that the cisPro(αR ) motif is preferred at helix N-termini because it allows the helix to participate in long-range interactions that may be structurally and functionally important.
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Affiliation(s)
- Rubin Dasgupta
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Himal K Ganguly
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - E K Modugula
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Gautam Basu
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
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15
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Buchenberg S, Schaudinnus N, Stock G. Hierarchical Biomolecular Dynamics: Picosecond Hydrogen Bonding Regulates Microsecond Conformational Transitions. J Chem Theory Comput 2016; 11:1330-6. [PMID: 26579778 DOI: 10.1021/ct501156t] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Biomolecules exhibit structural dynamics on a number of time scales, including picosecond (ps) motions of a few atoms, nanosecond (ns) local conformational transitions, and microsecond (μs) global conformational rearrangements. Despite this substantial separation of time scales, fast and slow degrees of freedom appear to be coupled in a nonlinear manner; for example, there is theoretical and experimental evidence that fast structural fluctuations are required for slow functional motion to happen. To elucidate a microscopic mechanism of this multiscale behavior, Aib peptide is adopted as a simple model system. Combining extensive molecular dynamics simulations with principal component analysis techniques, a hierarchy of (at least) three tiers of the molecule's free energy landscape is discovered. They correspond to chiral left- to right-handed transitions of the entire peptide that happen on a μs time scale, conformational transitions of individual residues that take about 1 ns, and the opening and closing of structure-stabilizing hydrogen bonds that occur within tens of ps and are triggered by sub-ps structural fluctuations. Providing a simple mechanism of hierarchical dynamics, fast hydrogen bond dynamics is found to be a prerequisite for the ns local conformational transitions, which in turn are a prerequisite for the slow global conformational rearrangement of the peptide. As a consequence of the hierarchical coupling, the various processes exhibit a similar temperature behavior which may be interpreted as a dynamic transition.
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Affiliation(s)
- Sebastian Buchenberg
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University , Freiburg, 79104 Germany
| | - Norbert Schaudinnus
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University , Freiburg, 79104 Germany
| | - Gerhard Stock
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University , Freiburg, 79104 Germany.,Freiburg Institute for Advanced Studies (FRIAS), Albert Ludwigs University , Freiburg, 79104 Germany
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16
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Crisma M, Peggion C, Moretto A, Banerjee R, Supakar S, Formaggio F, Toniolo C. The 2.0₅-helix in hetero-oligopeptides entirely composed of C(α,α)-disubstituted glycines with both side chains longer than methyls. Biopolymers 2016; 102:145-58. [PMID: 24307568 DOI: 10.1002/bip.22450] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 11/15/2013] [Accepted: 12/02/2013] [Indexed: 02/02/2023]
Abstract
The existence of the very uncommon, but potentially quite interesting, multiple, consecutive fully-extended conformation (2.0₅-helix) has been already clearly demonstrated in homo-oligopeptides based on quaternary α-amino acids with both side chains longer than methyls, but not cyclized on the α-carbon atom. To extend the scope of this research, in this work we investigated the occurrence of this flat 3D-structure in hetero-oligopeptides, each composed of two or three different residues of that class. The synthesis of a terminally protected peptide series to the tetrapeptide level was carried out by solution methods. The resulting oligomers were chemically and conformationally characterized. The data obtained point to an overwhelming population of the fully-extended conformation in CDCl3. However, a solvent-driven switch to a predominant 3₁₀-helical structure was seen in CD3CN. A delicate, local balance between these two conformations is confirmed to occur in the crystalline state. Molecular dynamics simulations in CHCl3 on a hetero-tetrapeptide converged to the fully-extended conformation even starting from the 3₁₀-helical structure.
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Affiliation(s)
- Marco Crisma
- Department of Chemistry, ICB, Padova Unit, CNR, University of Padova, 35131, Padova, Italy
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17
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Abstract
The ‘CαNN’ motif has an intrinsic affinity for the anions and can recognize anion through local interactions along with augmentation of the helical conformation at the motif segment.
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Affiliation(s)
- Tridip Sheet
- Maulana Abul Kalam Azad University of Technology (Formerly Known as West Bengal University of Technology)
- Kolkata – 700064
- India
| | - Raja Banerjee
- Maulana Abul Kalam Azad University of Technology (Formerly Known as West Bengal University of Technology)
- Kolkata – 700064
- India
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18
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Ruffoni A, Cavanna MV, Argentiere S, Locarno S, Pellegrino S, Gelmi ML, Clerici F. Aqueous self-assembly of short hydrophobic peptides containing norbornene amino acid into supramolecular structures with spherical shape. RSC Adv 2016. [DOI: 10.1039/c6ra17116h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The preparation and self-assembly of short hydrophobic peptides containing the non-coded norbornene amino acid is reported. The formation of a supramolecular assembly in water was assessed by TEM and DLS.
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Affiliation(s)
- Alessandro Ruffoni
- Università degli Studi di Milano
- Dipartimento di Scienze Farmaceutiche
- Sezione di Chimica Generale e Organica “Alessandro Marchesini”
- 20133 Milano
- Italy
| | | | | | - Silvia Locarno
- Università degli Studi di Milano
- Dipartimento di Scienze Farmaceutiche
- Sezione di Chimica Generale e Organica “Alessandro Marchesini”
- 20133 Milano
- Italy
| | - Sara Pellegrino
- Università degli Studi di Milano
- Dipartimento di Scienze Farmaceutiche
- Sezione di Chimica Generale e Organica “Alessandro Marchesini”
- 20133 Milano
- Italy
| | - Maria Luisa Gelmi
- Università degli Studi di Milano
- Dipartimento di Scienze Farmaceutiche
- Sezione di Chimica Generale e Organica “Alessandro Marchesini”
- 20133 Milano
- Italy
| | - Francesca Clerici
- Università degli Studi di Milano
- Dipartimento di Scienze Farmaceutiche
- Sezione di Chimica Generale e Organica “Alessandro Marchesini”
- 20133 Milano
- Italy
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19
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Chattopadhyay S, Ajani H, Basu G. Effect of introducing aib in a designed helical inhibitor of hdm2-p53 interaction: A molecular dynamics study. Biopolymers 2015; 106:51-61. [PMID: 26537425 DOI: 10.1002/bip.22761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 10/15/2015] [Accepted: 11/01/2015] [Indexed: 11/09/2022]
Abstract
Although p53 is an intrinsically disordered protein, upon binding to Hdm2, a short stretch (residues 19-25) comprising the binding epitope assumes a helical backbone. Because the allowed conformational space of α-aminoisobutyric acid (Aib) is restricted to only the helical basin, Aib-containing helical mimics of p53 (binding epitope) are expected to inhibit interaction between p53 and Hdm2 with a much stronger affinity than the wild type p53 peptide (binding epitope), due to the entropic advantage associated with Aib. However, the IC50 values for the disruption of p53-Hdm2 interaction by Aib-p53 peptides and wild type p53 peptide were found to be comparable (J. Peptide Res. 2002, 60:88-94). To understand why incorporation of Aib didn't substantially increase Hdm2 affinity of Aib-p53 peptides, a series of molecular dynamics simulations were performed. It was found that despite stabilizing a helical backbone in the unbound state, the Aib residues in Aib-p53 peptide arrested two functionally important side-chains (F19 and W23) in non-productive conformations, resulting in relative side-chain orientations of the binding triad F19-W23-L26 incompatible with the bound conformation. Therefore, although a Aib-induced pre-formed helical peptide backbone in the unbound state is expected to favor binding, the locked side-chain orientations of the binding triad in non-productive modes would disfavor binding. This study shows that when using Aib to design functionally important helical peptides, care must be taken to consider potential interactions between side-chains of neighboring residues and Aib in the unbound state.
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Affiliation(s)
- Sarbani Chattopadhyay
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
| | - Haresh Ajani
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India.,National Institute of Pharmaceutical Education and Research, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, 700032, India
| | - Gautam Basu
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata, 700054, India
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20
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Crisma M, De Zotti M, Formaggio F, Peggion C, Moretto A, Toniolo C. Handedness preference and switching of peptide helices. Part II: Helices based on noncodedα-amino acids. J Pept Sci 2015; 21:148-77. [DOI: 10.1002/psc.2743] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 12/19/2014] [Accepted: 12/19/2014] [Indexed: 12/27/2022]
Affiliation(s)
| | - Marta De Zotti
- Department of Chemistry; University of Padova; Padova Italy
| | - Fernando Formaggio
- ICB; Padova Unit; CNR Padova Italy
- Department of Chemistry; University of Padova; Padova Italy
| | | | - Alessandro Moretto
- ICB; Padova Unit; CNR Padova Italy
- Department of Chemistry; University of Padova; Padova Italy
| | - Claudio Toniolo
- ICB; Padova Unit; CNR Padova Italy
- Department of Chemistry; University of Padova; Padova Italy
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21
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Ahn HJ, Hong EY, Jin DH, Hong NJ. Highly Active Analogs of α-Factor and Their Activities Against Saccharomyces cerevisiae. B KOREAN CHEM SOC 2014. [DOI: 10.5012/bkcs.2014.35.5.1365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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22
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Arnhold FS, Linden A, Heimgartner H. Synthesis of Z-Protected Aib- and Phe(2Me)-Containing Pentapeptides and Their Crystal Structures. Helv Chim Acta 2014. [DOI: 10.1002/hlca.201400084] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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23
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Sheet T, Supakar S, Banerjee R. Conformational preference of 'CαNN' short peptide motif towards recognition of anions. PLoS One 2013; 8:e57366. [PMID: 23516403 PMCID: PMC3596363 DOI: 10.1371/journal.pone.0057366] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 01/21/2013] [Indexed: 11/18/2022] Open
Abstract
Among several ‘anion binding motifs’, the recently described ‘CαNN’ motif occurring in the loop regions preceding a helix, is conserved through evolution both in sequence and its conformation. To establish the significance of the conserved sequence and their intrinsic affinity for anions, a series of peptides containing the naturally occurring ‘CαNN’ motif at the N-terminus of a designed helix, have been modeled and studied in a context free system using computational techniques. Appearance of a single interacting site with negative binding free-energy for both the sulfate and phosphate ions, as evidenced in docking experiments, establishes that the ‘CαNN’ segment has an intrinsic affinity for anions. Molecular Dynamics (MD) simulation studies reveal that interaction with anion triggers a conformational switch from non-helical to helical state at the ‘CαNN’ segment, which extends the length of the anchoring-helix by one turn at the N-terminus. Computational experiments substantiate the significance of sequence/structural context and justify the conserved nature of the ‘CαNN’ sequence for anion recognition through “local” interaction.
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Affiliation(s)
- Tridip Sheet
- Department of Bioinformatics, West Bengal University of Technology, Salt Lake, Kolkata, India
| | - Subhrangshu Supakar
- Department of Bioinformatics, West Bengal University of Technology, Salt Lake, Kolkata, India
| | - Raja Banerjee
- Department of Bioinformatics, West Bengal University of Technology, Salt Lake, Kolkata, India
- * E-mail:
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24
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25
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Incorporation of noncanonical amino acids into Rosetta and use in computational protein-peptide interface design. PLoS One 2012; 7:e32637. [PMID: 22431978 PMCID: PMC3303795 DOI: 10.1371/journal.pone.0032637] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Accepted: 01/28/2012] [Indexed: 11/19/2022] Open
Abstract
Noncanonical amino acids (NCAAs) can be used in a variety of protein design contexts. For example, they can be used in place of the canonical amino acids (CAAs) to improve the biophysical properties of peptides that target protein interfaces. We describe the incorporation of 114 NCAAs into the protein-modeling suite Rosetta. We describe our methods for building backbone dependent rotamer libraries and the parameterization and construction of a scoring function that can be used to score NCAA containing peptides and proteins. We validate these additions to Rosetta and our NCAA-rotamer libraries by showing that we can improve the binding of a calpastatin derived peptides to calpain-1 by substituting NCAAs for native amino acids using Rosetta. Rosetta (executables and source), auxiliary scripts and code, and documentation can be found at (http://www.rosettacommons.org/).
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26
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Sheet T, Banerjee R. Sulfate ion interaction with 'anion recognition' short peptide motif at the N-terminus of an isolated helix: A conformational landscape. J Struct Biol 2010; 171:345-52. [PMID: 20570734 DOI: 10.1016/j.jsb.2010.06.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Revised: 05/26/2010] [Accepted: 06/01/2010] [Indexed: 10/19/2022]
Abstract
Anion-binding motifs in proteins are typically conserved in sequence and conformation. Crystal structural studies have shown that such motifs often occur in loop regions preceding a helix and interaction with the anions can induce their well defined conformational changes. In order to understand the properties of such motifs in isolation, we have synthesized an 18-residue chimeric polypeptide whose C-terminal part is a designed helix and its N-terminal consists of a C(alpha)NN anion binding structural motif containing residues Leu-Gly-Lys-Gln (residues 107-110 of protein DNA-glycosylase). We present evidence for the interaction of a sulfate (SO(4)(2-)) ion with the L-G-K-Q segment using complementary spectroscopic techniques. Moreover, upon interaction with SO(4)(2-) ion the N-terminal L-G-K-Q segment undergoes a non-helical to helical transition similar to what is observed in protein crystal structure. This work clearly demonstrates the "local" nature of anion binding and the accompanying conformational change that helps in understanding the influence of sequence/structural context of anion binding in proteins.
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Affiliation(s)
- Tridip Sheet
- Department of Bioinformatics, West Bengal University of Technology, BF-142, Sector-1, Salt Lake, Kolkata 700064, India
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