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Math BA, Waibl F, Lamp LM, Fernández‐Quintero ML, Liedl KR. Cross-linking disulfide bonds govern solution structures of diabodies. Proteins 2023; 91:1316-1328. [PMID: 37376973 PMCID: PMC10952579 DOI: 10.1002/prot.26509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/19/2023] [Indexed: 06/29/2023]
Abstract
In the last years, antibodies have emerged as a promising new class of therapeutics, due to their combination of high specificity with long serum half-life and low risk of side-effects. Diabodies are a popular novel antibody format, consisting of two Fv domains connected with short linkers. Like IgG antibodies, they simultaneously bind two target proteins. However, they offer altered properties, given their smaller size and higher rigidity. In this study, we conducted the-to our knowledge-first molecular dynamics (MD) simulations of diabodies and find a surprisingly high conformational flexibility in the relative orientation of the two Fv domains. We observe rigidifying effects through the introduction of disulfide bonds in the Fv -Fv interface and characterize the effect of different disulfide bond locations on the conformation. Additionally, we compare VH -VL orientations and paratope dynamics between diabodies and an antigen binding fragment (Fab) of the same sequence. We find mostly consistent structures and dynamics, indicating similar antigen binding properties. The most significant differences can be found within the CDR-H2 loop dynamics. Of all CDR loops, the CDR-H2 is located closest to the artificial Fv -Fv interface. All examined diabodies show similar VH -VL orientations, Fv -Fv packing and CDR loop conformations. However, the variant with a P14C-K64C disulfide bond differs most from the Fab in our measures, including the CDR-H3 loop conformational ensemble. This suggests altered antigen binding properties and underlines the need for careful validation of the disulfide bond locations in diabodies.
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Affiliation(s)
- Barbara A. Math
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnsbruckAustria
| | - Franz Waibl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnsbruckAustria
| | - Leonida M. Lamp
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnsbruckAustria
| | - Monica L. Fernández‐Quintero
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnsbruckAustria
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnsbruckAustria
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2
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Bingöl EN, Serçinoğlu O, Ozbek P. How do mutations and allosteric inhibitors modulate caspase-7 activity? A molecular dynamics study. J Biomol Struct Dyn 2018; 37:3456-3466. [DOI: 10.1080/07391102.2018.1517611] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Elif Naz Bingöl
- Department of Bioengineering, Institute of Pure and Applied Sciences, Marmara University, Istanbul, Turkey
| | - Onur Serçinoğlu
- Department of Bioengineering, Institute of Pure and Applied Sciences, Marmara University, Istanbul, Turkey
- Faculty of Engineering, Department of Bioengineering, Marmara University, Istanbul, Turkey
| | - Pemra Ozbek
- Faculty of Engineering, Department of Bioengineering, Marmara University, Istanbul, Turkey
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3
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Dutta S, Kundu S, Saha A, Nandi N. Dynamics of the active site loops in catalyzing aminoacylation reaction in seryl and histidyl tRNA synthetases. J Biomol Struct Dyn 2017; 36:878-892. [PMID: 28317434 DOI: 10.1080/07391102.2017.1301272] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Aminoacylation reaction is the first step of protein biosynthesis. The catalytic reorganization at the active site of aminoacyl tRNA synthetases (aaRSs) is driven by the loop motions. There remain lacunae of understanding concerning the catalytic loop dynamics in aaRSs. We analyzed the functional loop dynamics in seryl tRNA synthetase from Methanopyrus kandleri (mkSerRS) and histidyl tRNA synthetases from Thermus thermophilus (ttHisRS), respectively, using molecular dynamics. Results confirm that the motif 2 loop and other active site loops are flexible spots within the catalytic domain. Catalytic residues of the loops form a network of interaction with the substrates to form a reactive state. The loops undergo transitions between closed state and open state and the relaxation of the constituent residues occurs in femtosecond to nanosecond time scale. Order parameters are higher for constituent catalytic residues which form a specific network of interaction with the substrates to form a reactive state compared to the Gly residues within the loop. The development of interaction is supported from mutation studies where the catalytic domain with mutated loop exhibits unfavorable binding energy with the substrates. During the open-close motion of the loops, the catalytic residues make relaxation by ultrafast librational motion as well as fast diffusive motion and subsequently relax rather slowly via slower diffusive motion. The Gly residues act as a hinge to facilitate the loop closing and opening by their faster relaxation behavior. The role of bound water is analyzed by comparing implicit solvent-based and explicit solvent-based simulations. Loops fail to form catalytically competent geometry in absence of water. The present result, for the first time reveals the nature of the active site loop dynamics in aaRS and their influence on catalysis.
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Affiliation(s)
- Saheb Dutta
- a Department of Chemistry , University of Kalyani , Kalyani , 741235 , India
| | - Soumya Kundu
- a Department of Chemistry , University of Kalyani , Kalyani , 741235 , India
| | - Amrita Saha
- a Department of Chemistry , University of Kalyani , Kalyani , 741235 , India
| | - Nilashis Nandi
- a Department of Chemistry , University of Kalyani , Kalyani , 741235 , India
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4
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Childers MC, Towse CL, Daggett V. The effect of chirality and steric hindrance on intrinsic backbone conformational propensities: tools for protein design. Protein Eng Des Sel 2016; 29:271-80. [PMID: 27284086 DOI: 10.1093/protein/gzw023] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 05/11/2016] [Indexed: 01/30/2023] Open
Abstract
The conformational propensities of amino acids are an amalgamation of sequence effects, environmental effects and underlying intrinsic behavior. Many have attempted to investigate neighboring residue effects to aid in our understanding of protein folding and improve structure prediction efforts, especially with respect to difficult to characterize states, such as disordered or unfolded states. Host-guest peptide series are a useful tool in examining the propensities of the amino acids free from the surrounding protein structure. Here, we compare the distributions of the backbone dihedral angles (φ/ψ) of the 20 proteogenic amino acids in two different sequence contexts using the AAXAA and GGXGG host-guest pentapeptide series. We further examine their intrinsic behaviors across three environmental contexts: water at 298 K, water at 498 K, and 8 M urea at 298 K. The GGXGG systems provide the intrinsic amino acid propensities devoid of any conformational context. The alanine residues in the AAXAA series enforce backbone chirality, thereby providing a model of the intrinsic behavior of amino acids in a protein chain. Our results show modest differences in φ/ψ distributions due to the steric constraints of the Ala side chains, the magnitudes of which are dependent on the denaturing conditions. One of the strongest factors modulating φ/ψ distributions was the protonation of titratable side chains, and the largest differences observed were in the amino acid propensities for the rarely sampled αL region.
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Affiliation(s)
| | - Clare-Louise Towse
- Department of Bioengineering, University of Washington, Seattle, WA 98195-5013, USA
| | - Valerie Daggett
- Department of Bioengineering, University of Washington, Seattle, WA 98195-5013, USA
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5
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Zhou H, Yong J, Gao H, Yuan Z, Yang W, Tian Y, Wu Y. Loops Adjacent to Catalytic Region and Molecular Stability of Man1312. Appl Biochem Biotechnol 2016; 180:122-35. [PMID: 27193255 DOI: 10.1007/s12010-016-2087-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 04/11/2016] [Indexed: 10/21/2022]
Abstract
Hemicelluloses are the second major polysaccharides in nature and can be converted to ethanol product by a variety of enzymes including mannanases. Mannanase is an important enzyme that hydrolyses mannose-containing polysaccharides which are abundant in plants. An optimized mannanase could help to improve conversion process and make the technology efficiently and competitively. In this work, the effects of loops adjacent to active region on enzymic properties of Man1312 were investigated. Loop 6 and 10 are two loops neighboring to Man1312 catalytic region, and deletion mutagenesis and residue substitution were performed on both loops. Deletion on sites S145, Q148, N244, and S255 and substitution on sites N146, S147, S156, and T157 gave significant increased stability to enzyme. The quadruplet mutant ManD4I4 combined all the mutations and had higher optimal temperature and T m value by 5 and 4 °C than Man1312, respectively. From our data, we are able to conclude the loops of enzymes are important to design mutagenesis and obtain improved properties, especially the loops neighboring to catalytic region from tertiary structure. In our experiment, residue deletion and substitution on loops neighboring to catalytic region made significant improvement on enzyme properties.
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Affiliation(s)
- Haiyan Zhou
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Jie Yong
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Han Gao
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Zhihui Yuan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Wenjiao Yang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
| | - Yun Tian
- Key Lab of Agricultural Biochemistry and Biotransformation, Hunan Agricultural University, Changsha, 410128, China
| | - Yongyao Wu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China.
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6
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Kurkcuoglu Z, Findik D, Akten ED, Doruker P. How an Inhibitor Bound to Subunit Interface Alters Triosephosphate Isomerase Dynamics. Biophys J 2015; 109:1169-78. [PMID: 26190635 DOI: 10.1016/j.bpj.2015.06.031] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 05/18/2015] [Accepted: 06/08/2015] [Indexed: 10/23/2022] Open
Abstract
The tunnel region at triosephosphate isomerase (TIM)'s dimer interface, distant from its catalytic site, is a target site for certain benzothiazole derivatives that inhibit TIM's catalytic activity in Trypanosoma cruzi, the parasite that causes Chagas disease. We performed multiple 100-ns molecular-dynamics (MD) simulations and elastic network modeling (ENM) on both apo and complex structures to shed light on the still unclear inhibitory mechanism of one such inhibitor, named bt10. Within the time frame of our MD simulations, we observed stabilization of aromatic clusters at the dimer interface and enhancement of intersubunit hydrogen bonds in the presence of bt10, which point to an allosteric effect rather than destabilization of the dimeric structure. The collective dynamics dictated by the topology of TIM is known to facilitate the closure of its catalytic loop over the active site that is critical for substrate entrance and product release. We incorporated the ligand's effect on vibrational dynamics by applying mixed coarse-grained ENM to each one of 54,000 MD snapshots. Using this computationally efficient technique, we observed altered collective modes and positive shifts in eigenvalues due to the constraining effect of bt10 binding. Accordingly, we observed allosteric changes in the catalytic loop's dynamics, flexibility, and correlations, as well as the solvent exposure of catalytic residues. A newly (to our knowledge) introduced technique that performs residue-based ENM scanning of TIM revealed the tunnel region as a key binding site that can alter global dynamics of the enzyme.
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Affiliation(s)
- Zeynep Kurkcuoglu
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, Istanbul, Turkey
| | - Doga Findik
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, Istanbul, Turkey
| | - Ebru Demet Akten
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Cibali, Istanbul, Turkey
| | - Pemra Doruker
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, Istanbul, Turkey.
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7
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Dutta S, Nandi N. Dynamics of the Active Sites of Dimeric Seryl tRNA Synthetase from Methanopyrus kandleri. J Phys Chem B 2015; 119:10832-48. [PMID: 25794108 DOI: 10.1021/jp511585w] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Saheb Dutta
- Department
of Chemistry, University of Kalyani, Kalyani, Nadia, West Bengal 741235, India
| | - Nilashis Nandi
- Department
of Chemistry, University of Kalyani, Kalyani, Nadia, West Bengal 741235, India
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8
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Affiliation(s)
- Bettina M. Nestl
- Institute
of Technical Biochemistry, University of Stuttgart, Allmandring
31, 70569 Stuttgart, Germany
| | - Bernhard Hauer
- Institute
of Technical Biochemistry, University of Stuttgart, Allmandring
31, 70569 Stuttgart, Germany
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9
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Weiser BP, Salari R, Eckenhoff RG, Brannigan G. Computational investigation of cholesterol binding sites on mitochondrial VDAC. J Phys Chem B 2014; 118:9852-60. [PMID: 25080204 PMCID: PMC4141696 DOI: 10.1021/jp504516a] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
The
mitochondrial voltage-dependent anion channel (VDAC) allows
passage of ions and metabolites across the mitochondrial outer membrane.
Cholesterol binds mammalian VDAC, and we investigated the effects
of binding to human VDAC1 with atomistic molecular dynamics simulations
that totaled 1.4 μs. We docked cholesterol to specific sites
on VDAC that were previously identified with NMR, and we tested the
reliability of multiple docking results in each site with simulations.
The most favorable binding modes were used to build a VDAC model with
cholesterol occupying five unique sites, and during multiple 100 ns
simulations, cholesterol stably and reproducibly remained bound to
the protein. For comparison, VDAC was simulated in systems with identical
components but with cholesterol initially unbound. The dynamics of
loops that connect adjacent β-strands were most affected by
bound cholesterol, with the averaged root-mean-square fluctuation
(RMSF) of multiple residues altered by 20–30%. Cholesterol
binding also stabilized charged residues inside the channel and localized
the surrounding electrostatic potentials. Despite this, ion diffusion
through the channel was not significantly affected by bound cholesterol,
as evidenced by multi-ion potential of mean force measurements. Although
we observed modest effects of cholesterol on the open channel, our
model will be particularly useful in experiments that investigate
how cholesterol affects VDAC function under applied electrochemical
forces and also how other ligands and proteins interact with the channel.
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Affiliation(s)
- Brian P Weiser
- Department of Anesthesiology and Critical Care and ‡Department of Pharmacology, University of Pennsylvania Perelman School of Medicine , Philadelphia, Pennsylvania 19104, United States
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10
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Substrate Effect on Catalytic Loop and Global Dynamics of Triosephosphate Isomerase. ENTROPY 2013. [DOI: 10.3390/e15031085] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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