Structure of catalytic domain of Matriptase in complex with Sunflower trypsin inhibitor-1
© Yuan et al; licensee BioMed Central Ltd. 2011
Received: 7 February 2011
Accepted: 22 June 2011
Published: 22 June 2011
Matriptase is a type II transmembrane serine protease that is found on the surfaces of epithelial cells and certain cancer cells. Matriptase has been implicated in the degradation of certain extracellular matrix components as well as the activation of various cellular proteins and proteases, including hepatocyte growth factor and urokinase. Sunflower trypsin inhibitor-1 (SFTI-1), a cyclic peptide inhibitor originally isolated from sunflower seeds, exhibits potent inhibitory activity toward matriptase.
We have engineered and produced recombinant proteins of the matriptase protease domain, and have determined the crystal structures of the protease:SFTI-1 complex at 2.0 Å as well as the protease:benzamidine complex at 1.2 Å. These structures elaborate the structural basis of substrate selectivity of matriptase, and show that the matriptase S1 substrate specificity pocket is larger enough to allow movement of benzamidine inside the S1 pocket. Our study also reveals that SFTI-1 binds to matriptase in a way similar to its binding to trypsin despite the significantly different isoelectric points of the two proteins (5.6 vs. 8.2).
This work helps to define the structural basis of substrate specificity of matriptase and the interactions between the inhibitor and protease. The complex structure also provides a structural template for designing new SFTI-1 derivatives with better potency and selectivity against matriptase and other proteases.
Matriptase is a type II transmembrane serine protease of the S1 trypsin-like family. Matriptase activity is down-regulated by its physiological inhibitor, hepatocyte growth factor activator inhibitor-1 (HAI-1) [1–3]. Matriptase is expressed in most epithelial cells and plays essential roles in the establishment and maintenance of epithelial integrity. New evidence suggests that matriptase is also expressed on mast cells, peripheral blood monocytes and B cells, implicating matriptase in the physiological and pathologic functions of these cells [4–6]. Knock down studies in mice have shown that the protease is important in postnatal survival, epidermal barrier formation, hair follicle growth and thymichomeostasis . At the same time, genetic studies using zebra fish and mice have indicated that the activity of matriptase is critical for tissue-integrity and function, and must be strictly controlled by HAI-1 [8–11].
The catalytic domain of matriptase is tethered to the cell surface via its N-terminal signal anchor, linked by a sea urchin sperm protein/enterokinase/agrin (SEA) domain, two tandem complement/urchin embryonic growth factor/bone morphogenetic protein (CUB) domains, and four tandem low-density lipoprotein receptor class A (LDLRA) domains. Interestingly, matriptase activation does not depend on other active proteases. Instead, several lines of evidence have indicated that matriptase undergoes autoactivation through a mechanism relying on its own catalytic triad and requires its non-catalytic domains as well as the presence of its cognate inhibitor HAI-1 [12, 13]. Although the autoactivation mechanism is not fully understood, one study has showed that matriptase could be activated by acidification, and suggested that matriptase might act as an early response to cellular acidosis . Once activated, matriptase has only short time to cleave and activate its substrates since the protease will be quickly inhibited by HAI-1.
Matriptase activates a number of substrates, including G-protein-coupled protease-activated receptor 2, urokinase plasminogen activator and pro-hepatocyte growth factor [15, 16]. Recently, it has been demonstrated that matriptase could also activate prekallikren either in vitro or in vivo. Matriptase is recognized as a cancer-associated protease since the activation of urokinase plasminogen activator and/or pro-hepatocyte growth factor has been implicated in cancer invasion and metastasis (reviewed in ). In addition, matriptase has been found to be upregulated in various forms of cancers including breast, cervical, ovarian, liver, and prostate cancers. It has been demonstrated that the level of expression of matriptase correlates with the tumor stage and malignancy of breast, cervical, ovarian and prostate cancers [19–21]. In some of these cancers, the ratios of the protease relative to its inhibitor HAI-1 are unbalanced; suggesting that strict regulation of matriptase by HAI-1 is required to prevent carcinogenesis. A recent study showed that matriptase orthotopically overexpressed at modest levels in the skin of transgenic mice caused spontaneous squamous cell carcinoma, potentiated chemical carcinogenesis, and supported both ras-dependent and -independent carcinogenesis, whereas the overexpression of HAI-1 could nullify these oncogenic effects . In addition to its role in cancers, recent studies have suggested that matriptase also has potential implications in a variety of diseases including osteroarthritis, atherosclerosis, and skin disorders like autosomal recessive ichthyosis and hypotrichosis (ARIH) [4, 23–26]. Taken together, matriptase has emerged as an attractive target for the development of anti-metastasis therapy as well as treatment for many other diseases.
Sunflower trypsin inhibitor-1 (SFTI-1), a 14-amino acid cyclic peptide, is originally isolated from sunflower seeds and characterized as the most potent peptidic inhibitor of trypsin (Ki = 0.1 nM and 1 nM from two independent studies) [27, 28]. A later study finds that synthetic SFTI-1 also exhibits very potent matriptase inhibitory activity (Ki = 0.92 nM) . To evaluate the structural basis of the high inhibitory effect of SFTI-1 to matriptase, we have determined the X-ray structure of matriptase in complex with SFTI-1. We have also determined the high-resolution structure of matriptase:benzamidine complex for structural comparison. The crystal structures provide new insights into the molecular basis of matriptase inhibition and this information might facilitate future design of more potent and selective peptide inhibitors using SFTI-1 as template.
Results and Discussion
Engineering of recombinant matriptase catalytic domain in P. pastoris for structural study
For our structural studies, we constructed a recombinant protease domain of matriptase (residue 615 to 854 of the EXPASY entry Q9Y5Y6) with a point mutation N164Q (chymotrypsin numbering will be used throughout the paper starting from here), which is referred as β-matriptase-N164Q. The point mutation removes a glycosylation site (N164) and allows the protein to be purified to homogeneity. Another unique feature of the current design of the expression scheme is that the secreted recombinant matriptase protease domain is an active serine protease without the need of being activated. This is due to the processing of the secreted protein by an endogenous kex2 enzyme of P. pastoris that generates the genuine N-terminus of matriptase protease domain and allows the correct folding of the protease into its active form. We have used such approach to generate a number of active proteases including urokinase-type plasminogen activator , tissue-type plasminogen activator and coagulation factor XIa (to be published), suggesting that our method can be widely adapted for the expression of different active proteases.
Structure of β-matriptase-N164Q:benzamidine shows benzamidine mobility
Interactions between matriptase and SFTI-1 at the active site
Hydrogen bonds between matriptase (chymotrypsin numbering) and SFTI-1
Comparison of the conformations of matriptase in the benzamidine- and SFTI-1-bound forms reveals that they are nearly identical except the side chain of Phe99 at the S2 subsite, which will be discussed later, and Gln192 at the S3 subsite. Gln192 side chain is solvent-exposed in the benzamidine-bound structure and forms the lining of the extended active site groove. However, it undergoes a major conformational change to "bend inward" to accommodate SFTI-1 and hydrogen bonds with the backbone carbonyl of Thr4 of the cyclic inhibitor in a manner similar to that in the BPTI-bound matriptase structure.
Substrate selectivity of matriptase
Calculated binding energies of cation-π interactions between matriptase and SFTI-1 
SFTI-1 side chain
Matriptase aromatic side chain
E(van der Waals) (kcal/mol)
Comparison of SFTI-1 binding to matriptase and trypsin
Implication for future inhibitor design
The current structure provides a template for further improvement of SFTI-1. For instance, non-polar residues like Ile7 and Ile10 are good candidates for modifications of this bicyclic peptide to improve its binding enthalpy. Ile10 is located in a cavity formed by the surface exposed insertion loops (loops 66 and 99) of matriptase and is proximal to the active site. However, it does not make any direct contacts with residues from the protease. Previous work by Li et al. shows that Ile10 plays an important role in the selectivity of the inhibitor as its replacement by a more polar and bulky glutamine improves the compound selectivity for matriptase versus thrombin by >1073 fold . Based on the electrostatic surface potential of matriptase calculated from our structure, the modification of SFTI-1 Ile10 to a positively charged amino acid might fit the cavity more tightly and provide a favorable enthalpy. However, increasing flexibility of the inhibitor might result in loss of configurational entropy upon binding, as illustrated by the higher Ki of the Gln10 derivative of SFTI-1 . Therefore, flexible amino acids like lysine and arginine should be avoided for the substitution and small positively charged unnatural amino acids such as diaminopropionic acid or diaminobutyric acid may be used instead. These small side chains will likely favor the interaction with Asp96 without disrupting the conformation of the catalytic triad and improves the enthalpy of binding while minimizing the entropy penalty . Similarly, Ile7 lies on top of a groove adjacent to the catalytic cleft of matriptase and its sole direct interaction with matriptase is through weak van der Waals interaction with Ile41. We believe our suggested strategy for the modification of Ile10 can also be applied to Ile7. Together, the combination of modifications at Ile7 and Ile10 should improve the inhibitory activity of SFTI-1 towards matriptase.
SFTI-1 is originally isolated and characterized as a potent trypsin inhibitor. It has also been synthesized by Roller's group and shown to exhibit potent inhibitory effect against matriptase. The same group also investigated the structural basis of the high inhibitory activity of SFTI-1 using molecular modeling study and obtained information that aids the design and synthesis of new SFTI-1 analogs. While modification to stabilize the disulfide bond within the cyclic peptide maintains the compound's inhibitory potency and selectivity of matriptase versus thrombin, replacement of Ile10 with the more polar glutamine improves selectivity towards matriptase at the expense of weakening its inhibitory activity. Nevertheless, none of the modified inhibitors show improvement in binding affinity to matriptase. This major drawback can now be overcome by better aid from the structural information of an experimentally obtained structure of matriptase:SFTI-1 complex. This work helps to define the structural basis of substrate specificity of matriptase and provides more details in the interactions between the inhibitor and protease. Our structure also reveals the structural difference between the SFTI-1 bound matriptase and trypsin complexes to allow development of more potent and selective inhibitors for matriptase.
Recombinant protein expression and Purification
The matriptase N164Q (chymotrypsin numbering) catalytic domain mutant was first generated by site-directed mutagenesis using cDNA encoding the entire protease domain of human matriptase as template. The cDNA was then amplified by PCR using primers containing XhoI and SalI restriction sites. The purified PCR products were digested with XhoI and SalI and subcloned into the XhoI-SalI sites of the Pichia pastoris (P. pastoris) expression vector pPICZαA (Invitrogen). Plasmid DNAs were linearized with the restriction enzyme SacI prior to transformation into P. pastoris strain X-33. Recombinant matriptases were expressed in P. pastoris according to the manufacturer's recommendations. P. pastoris expression medium was concentrated 10-20 fold using a Millipore concentrator (8000 Da MWCO membrane) and pH was adjusted to 7.4. The concentrated medium was applied onto a benzamidine column (GE Healthcare) equilibrated with 50 mM Tris, 0.5 M NaCl, pH7.4, and eluted with 100 mM glycine, pH 3.0. The elution fractions were neutralized with 1 M Tris pH 9 immediately. Fractions containing matriptase activity were pooled and concentrated, and passed through MonoQ column (Amersham Biosciences, Inc.) pre-equilibrated with 40 mM Tris. The protein was eluted in a buffer containing 40 mM Tris, pH7.4 with a 0-0.4 M NaCl gradient. Fractions containing protein were pooled and concentrated to 5 mg/ml. Aliquots of the purified protein were frozen at 193 K for crystallization experiments.
Crystallization of β-matriptase-N164Q complex with its inhibitors
For protein crystallization, β-matriptase-N164Q:benzamidine complexes were mixed at 1:10 ratio, and crystallized by the hanging-drop vapor diffusion method with a precipitant solution of 0.1 M Tris, pH 8.0, 1.5 M ammonium sulfate, 3% ethanol. SFTI-1 was synthesized by solid state synthesis as previously reported . The complex of β-matriptase-N164Q with SFTI-1 was crystallized with a precipitant condition of 22% polyethylene glycol 8000, 0.1 M Tris pH 8 and 20 mM CaCl2.
Data collection, structure solution and refinement
Statistics of X-ray diffraction data collection and structure refinement
Cell parameters (Å)
66.9, 141.7, 52.0
75.9, 75.9, 94.1
Bond length (Å)
Bond angles (°)
Mean B factors (Å2)
Ramachandran plot, % residues in regions:
PDB ID Code
bovine pancreatic trypsin inhibitor
hepatocyte growth factor activator inhibitor-1
Protein Data Bank
root mean square deviation
Sunflower trypsin inhibitor-1.
The work was supported by Natural Science Foundation of China (30770429, 30811130467) and Fujian Province (2009J05091).
- Tanimoto H, Underwood LJ, Wang Y, Shigemasa K, Parmley TH, O'Brien TJ: Ovarian tumor cells express a transmembrane serine protease: a potential candidate for early diagnosis and therapeutic intervention. Tumour Biol 2001, 22(2):104–114. 10.1159/000050604View ArticlePubMedGoogle Scholar
- Lin CY, Anders J, Johnson M, Sang QA, Dickson RB: Molecular cloning of cDNA for matriptase, a matrix-degrading serine protease with trypsin-like activity. J Biol Chem 1999, 274(26):18231–18236. 10.1074/jbc.274.26.18231View ArticlePubMedGoogle Scholar
- Takeuchi T, Shuman MA, Craik CS: Reverse biochemistry: use of macromolecular protease inhibitors to dissect complex biological processes and identify a membrane-type serine protease in epithelial cancer and normal tissue. Proc Natl Acad Sci USA 1999, 96(20):11054–11061. 10.1073/pnas.96.20.11054PubMed CentralView ArticlePubMedGoogle Scholar
- Milner JM, Patel A, Davidson RK, Swingler TE, Desilets A, Young DA, Kelso EB, Donell ST, Cawston TE, Clark IM, et al.: Matriptase is a novel initiator of cartilage matrix degradation in osteoarthritis. Arthritis Rheum 2010, 62(7):1955–1966.PubMedGoogle Scholar
- Kilpatrick LM, Harris RL, Owen KA, Bass R, Ghorayeb C, Bar-Or A, Ellis V: Initiation of plasminogen activation on the surface of monocytes expressing the type II transmembrane serine protease matriptase. Blood 2006, 108(8):2616–2623. 10.1182/blood-2006-02-001073View ArticlePubMedGoogle Scholar
- Cheng MF, Jin JS, Wu HW, Chiang PC, Sheu LF, Lee HS: Matriptase expression in the normal and neoplastic mast cells. Eur J Dermatol 2007, 17(5):375–380.PubMedGoogle Scholar
- List K, Haudenschild CC, Szabo R, Chen W, Wahl SM, Swaim W, Engelholm LH, Behrendt N, Bugge TH: Matriptase/MT-SP1 is required for postnatal survival, epidermal barrier function, hair follicle development, and thymic homeostasis. Oncogene 2002, 21(23):3765–3779. 10.1038/sj.onc.1205502View ArticlePubMedGoogle Scholar
- Szabo R, Molinolo A, List K, Bugge TH: Matriptase inhibition by hepatocyte growth factor activator inhibitor-1 is essential for placental development. Oncogene 2007, 26(11):1546–1556. 10.1038/sj.onc.1209966View ArticlePubMedGoogle Scholar
- Szabo R, Kosa P, List K, Bugge TH: Loss of matriptase suppression underlies spint1 mutation-associated ichthyosis and postnatal lethality. Am J Pathol 2009, 174(6):2015–2022. 10.2353/ajpath.2009.090053PubMed CentralView ArticlePubMedGoogle Scholar
- Fan B, Brennan J, Grant D, Peale F, Rangell L, Kirchhofer D: Hepatocyte growth factor activator inhibitor-1 (HAI-1) is essential for the integrity of basement membranes in the developing placental labyrinth. Dev Biol 2007, 303(1):222–230. 10.1016/j.ydbio.2006.11.005View ArticlePubMedGoogle Scholar
- Carney TJ, von der Hardt S, Sonntag C, Amsterdam A, Topczewski J, Hopkins N, Hammerschmidt M: Inactivation of serine protease Matriptase1a by its inhibitor Hai1 is required for epithelial integrity of the zebrafish epidermis. Development 2007, 134(19):3461–3471. 10.1242/dev.004556View ArticlePubMedGoogle Scholar
- Oberst MD, Williams CA, Dickson RB, Johnson MD, Lin CY: The activation of matriptase requires its noncatalytic domains, serine protease domain, and its cognate inhibitor. J Biol Chem 2003, 278(29):26773–26779. 10.1074/jbc.M304282200View ArticlePubMedGoogle Scholar
- Lee MS, Tseng IC, Wang Y, Kiyomiya K, Johnson MD, Dickson RB, Lin CY: Autoactivation of matriptase in vitro: requirement for biomembrane and LDL receptor domain. Am J Physiol Cell Physiol 2007, 293(1):C95–105. 10.1152/ajpcell.00611.2006View ArticlePubMedGoogle Scholar
- Tseng IC, Xu H, Chou FP, Li G, Vazzano AP, Kao JP, Johnson MD, Lin CY: Matriptase activation, an early cellular response to acidosis. J Biol Chem 2010, 285(5):3261–3270. 10.1074/jbc.M109.055640PubMed CentralView ArticlePubMedGoogle Scholar
- Lee SL, Dickson RB, Lin CY: Activation of hepatocyte growth factor and urokinase/plasminogen activator by matriptase, an epithelial membrane serine protease. J Biol Chem 2000, 275(47):36720–36725. 10.1074/jbc.M007802200View ArticlePubMedGoogle Scholar
- Takeuchi T, Harris JL, Huang W, Yan KW, Coughlin SR, Craik CS: Cellular localization of membrane-type serine protease 1 and identification of protease-activated receptor-2 and single-chain urokinase-type plasminogen activator as substrates. J Biol Chem 2000, 275(34):26333–26342. 10.1074/jbc.M002941200View ArticlePubMedGoogle Scholar
- Sales K, Masedunskas A, Bey A, Rasmussen A, Weigert R, List K, Szabo R, Overbeek P, Bugge T: Matriptase initiates activation of epidermal pro-kallikrein and disease onset in a mouse model of Netherton syndrome. Nat Genet 2010, 42(8):676–683. 10.1038/ng.629PubMed CentralView ArticlePubMedGoogle Scholar
- List K: Matriptase: a culprit in cancer? Future Oncol 2009, 5(1):97–104. 10.2217/147966184.108.40.206View ArticlePubMedGoogle Scholar
- Saleem M, Adhami VM, Zhong W, Longley BJ, Lin CY, Dickson RB, Reagan-Shaw S, Jarrard DF, Mukhtar H: A novel biomarker for staging human prostate adenocarcinoma: overexpression of matriptase with concomitant loss of its inhibitor, hepatocyte growth factor activator inhibitor-1. Cancer Epidemiol Biomarkers Prev 2006, 15(2):217–227. 10.1158/1055-9965.EPI-05-0737View ArticlePubMedGoogle Scholar
- Lee JW, Yong Song S, Choi JJ, Lee SJ, Kim BG, Park CS, Lee JH, Lin CY, Dickson RB, Bae DS: Increased expression of matriptase is associated with histopathologic grades of cervical neoplasia. Hum Pathol 2005, 36(6):626–633. 10.1016/j.humpath.2005.03.003View ArticlePubMedGoogle Scholar
- Tanimoto H, Shigemasa K, Tian X, Gu L, Beard JB, Sawasaki T, O'Brien TJ: Transmembrane serine protease TADG-15 (ST14/Matriptase/MT-SP1): expression and prognostic value in ovarian cancer. Br J Cancer 2005, 92(2):278–283.PubMed CentralPubMedGoogle Scholar
- List K, Szabo R, Molinolo A, Sriuranpong V, Redeye V, Murdock T, Burke B, Nielsen BS, Gutkind JS, Bugge TH: Deregulated matriptase causes ras-independent multistage carcinogenesis and promotes ras-mediated malignant transformation. Genes Dev 2005, 19(16):1934–1950. 10.1101/gad.1300705PubMed CentralView ArticlePubMedGoogle Scholar
- Seitz I, Hess S, Schulz H, Eckl R, Busch G, Montens HP, Brandl R, Seidl S, Schomig A, Ott I: Membrane-type serine protease-1/matriptase induces interleukin-6 and -8 in endothelial cells by activation of protease-activated receptor-2: potential implications in atherosclerosis. Arterioscler Thromb Vasc Biol 2007, 27(4):769–775. 10.1161/01.ATV.0000258862.61067.14View ArticlePubMedGoogle Scholar
- Basel-Vanagaite L, Attia R, Ishida-Yamamoto A, Rainshtein L, Ben Amitai D, Lurie R, Pasmanik-Chor M, Indelman M, Zvulunov A, Saban S, et al.: Autosomal recessive ichthyosis with hypotrichosis caused by a mutation in ST14, encoding type II transmembrane serine protease matriptase. Am J Hum Genet 2007, 80(3):467–477. 10.1086/512487PubMed CentralView ArticlePubMedGoogle Scholar
- Avrahami L, Maas S, Pasmanik-Chor M, Rainshtein L, Magal N, Smitt J, van Marle J, Shohat M, Basel-Vanagaite L: Autosomal recessive ichthyosis with hypotrichosis syndrome: further delineation of the phenotype. Clin Genet 2008, 74(1):47–53. 10.1111/j.1399-0004.2008.01006.xView ArticlePubMedGoogle Scholar
- Alef T, Torres S, Hausser I, Metze D, Tursen U, Lestringant GG, Hennies HC: Ichthyosis, follicular atrophoderma, and hypotrichosis caused by mutations in ST14 is associated with impaired profilaggrin processing. J Invest Dermatol 2009, 129(4):862–869. 10.1038/jid.2008.311View ArticlePubMedGoogle Scholar
- Long YQ, Lee SL, Lin CY, Enyedy IJ, Wang S, Li P, Dickson RB, Roller PP: Synthesis and evaluation of the sunflower derived trypsin inhibitor as a potent inhibitor of the type II transmembrane serine protease, matriptase. Bioorg Med Chem Lett 2001, 11(18):2515–2519. 10.1016/S0960-894X(01)00493-0View ArticlePubMedGoogle Scholar
- Luckett S, Garcia RS, Barker JJ, Konarev AV, Shewry PR, Clarke AR, Brady RL: High-resolution structure of a potent, cyclic proteinase inhibitor from sunflower seeds. J Mol Biol 1999, 290(2):525–533. 10.1006/jmbi.1999.2891View ArticlePubMedGoogle Scholar
- Zhao G, Yuan C, Wind T, Huang Z, Andreasen PA, Huang M: Structural basis of specificity of a peptidyl urokinase inhibitor, upain-1. J Struct Biol 2007, 160(1):1–10. 10.1016/j.jsb.2007.06.003View ArticlePubMedGoogle Scholar
- Friedrich R, Fuentes-Prior P, Ong E, Coombs G, Hunter M, Oehler R, Pierson D, Gonzalez R, Huber R, Bode W, et al.: Catalytic domain structures of MT-SP1/matriptase, a matrix-degrading transmembrane serine proteinase. J Biol Chem 2002, 277(3):2160–2168. 10.1074/jbc.M109830200View ArticlePubMedGoogle Scholar
- Li Y, Huang Q, Zhang S, Liu S, Chi C, Tang Y: Studies on an artificial trypsin inhibitor peptide derived from the mung bean trypsin inhibitor: chemical synthesis, refolding, and crystallographic analysis of its complex with trypsin. J Biochem 1994, 116(1):18–25.PubMedGoogle Scholar
- Tsunogae Y, Tanaka I, Yamane T, Kikkawa J, Ashida T, Ishikawa C, Watanabe K, Nakamura S, Takahashi K: Structure of the trypsin-binding domain of Bowman-Birk type protease inhibitor and its interaction with trypsin. J Biochem 1986, 100(6):1637–1646.PubMedGoogle Scholar
- Werner MH, Wemmer DE: Three-dimensional structure of soybean trypsin/chymotrypsin Bowman-Birk inhibitor in solution. Biochemistry 1992, 31(4):999–1010. 10.1021/bi00119a008View ArticlePubMedGoogle Scholar
- Gallivan JP, Dougherty DA: Cation-pi interactions in structural biology. Proc Natl Acad Sci USA 1999, 96(17):9459–9464. 10.1073/pnas.96.17.9459PubMed CentralView ArticlePubMedGoogle Scholar
- Crowley PB, Golovin A: Cation-pi interactions in protein-protein interfaces. Proteins 2005, 59(2):231–239. 10.1002/prot.20417View ArticlePubMedGoogle Scholar
- Li P, Jiang S, Lee SL, Lin CY, Johnson MD, Dickson RB, Michejda CJ, Roller PP: Design and synthesis of novel and potent inhibitors of the type II transmembrane serine protease, matriptase, based upon the sunflower trypsin inhibitor-1. J Med Chem 2007, 50(24):5976–5983. 10.1021/jm0704898View ArticlePubMedGoogle Scholar
- Chang CE, Chen W, Gilson MK: Ligand configurational entropy and protein binding. Proc Natl Acad Sci USA 2007, 104(5):1534–1539. 10.1073/pnas.0610494104PubMed CentralView ArticlePubMedGoogle Scholar
- Shakkottai VG, Regaya I, Wulff H, Fajloun Z, Tomita H, Fathallah M, Cahalan MD, Gargus JJ, Sabatier JM, Chandy KG: Design and characterization of a highly selective peptide inhibitor of the small conductance calcium-activated K+ channel, SkCa2. J Biol Chem 2001, 276(46):43145–43151. 10.1074/jbc.M106981200View ArticlePubMedGoogle Scholar
- Korsinczky MLJ, Schirra HJ, Rosengren KJ, West J, Condie BA, Otvos L, Anderson MA, Craik DJ: Solution structures by 1H NMR of the novel cyclic trypsin inhibitor SFTI-1 from sunflower seeds and an acyclic permutant. J Mol Biol 2001, 311(3):579–591. 10.1006/jmbi.2001.4887View ArticlePubMedGoogle Scholar
- Vagin A, Teplyakov A: MOLREP: an automated program for molecular replacement. J Appl Cryst 1997, 30: 1022–1025. 10.1107/S0021889897006766View ArticleGoogle Scholar
- CCP4: The CCP4 suite; Programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 1994, 50: 760–763. 10.1107/S0907444994003112View ArticleGoogle Scholar
- Murshudov GN, Vagin AA, Dodson EJ: Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 1997, 53(Pt 3):240–255.View ArticlePubMedGoogle Scholar
- Adams PD, Afonine PV, Bunkoczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung L-W, Kapral GJ, Grosse-Kunstleve RW, et al.: PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 2010, 66(2):213–221. 10.1107/S0907444909052925PubMed CentralView ArticlePubMedGoogle Scholar
- Emsley P, Cowtan K: Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 2004, 60: 2126–2132. 10.1107/S0907444904019158View ArticlePubMedGoogle Scholar
- Painter J, Merritt EA: TLSMD web server for the generation of multi-group TLS models. J Appl Crystallogr 2006, 39: 109–111. 10.1107/S0021889805038987View ArticleGoogle Scholar
- Laskowski RA, MacArthur MW, Mass DS, Thornton JM: PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 1993, 26: 283–291. 10.1107/S0021889892009944View ArticleGoogle Scholar
- DeLano WL: The PyMol Molecular Graphics system. DeLano scientific, San Carlos, CA, USA; 2002.Google Scholar
- Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA: Electrostatics of nanosystems: Application to microtubules and the ribosome. Proc Natl Acad Sci USA 2001, 98: 10037–10041. 10.1073/pnas.181342398PubMed CentralView ArticlePubMedGoogle Scholar
- Jin L, Pandey P, Babine RE, Weaver DT, Abdel-Meguid SS, Strickler JE: Mutation of surface residues to promote crystallization of activated factor XI as a complex with benzamidine: an essential step for the iterative structure-based design of factor XI inhibitors. Acta Crystallogr D Biol Crystallogr 2005, 61: 1418–1425. 10.1107/S0907444905024340View ArticlePubMedGoogle Scholar