33:
481:
404:
392:
380:
368:
1196:
492:
at the bottom of the table. Except for strands 1 and 6, all strands are antiparallel. The parallel interaction between strands 1 and 6 accounts for the different appearance of the hydrogen bonding pattern. (Some arrows are missing because not all of the hydrogen bonds expected were identified. Non-standard amino acids are indicated with "?") The side chains that point to the outside of the barrel are in bold.
204:
77:
302:, is lined with charged residues arranged so that the positive and negative charges appear on opposite sides of the pore. A long loop between two beta strands partially occludes the central channel; the exact size and conformation of the loop helps in discriminating between molecules passing through the transporter.
491:
The inter-strand hydrogen bonds can be summarised in a table. Each column contains the residues in one strand (strand 1 is repeated in the last column). The arrows indicate the hydrogen bonds that were identified in the figures. The relative direction of each strand is indicated by the "+" and "-"
446:
A piece of paper can be formed into a cylinder by bringing opposite sides together. The two edges come together to form a line. Shear can be created by sliding the two edges parallel to that line. Likewise, a beta barrel can be formed by bringing the edges of a beta sheet together to form a
495:
If no shear were present in this barrel, then residue 12 V, say, in strand 1 should end up in the last strand at the same level as it started at. However, because of shear, 12 V is not at the same level: it is 14 residues higher than it started at, so its shear number,
258:
or barrel, also known as the Swiss roll, typically comprises eight beta strands arranged in two four-stranded sheets. Adjacent strands along the sequence alternate between the two sheets, such that they are "wrapped" in three dimensions to form a barrel shape.
310:
Beta barrels also function within endosymbiont derived organelles such as mitochondria and chloroplasts to transport proteins. Within the mitochondrion two complexes exist with beta barrels serving as the pore forming subunit, Tom40 of the
333:
Lipocalins are typically eight-stranded up-and-down beta barrel proteins that are secreted into the extracellular environment. A distinctive feature is their ability to bind and transport small hydrophobic molecules in the barrel
477:. This protein was chosen because the beta barrel contains both parallel and antiparallel strands. To determine which amino acid residues are adjacent in the beta strands, the location of hydrogen bonds is determined.
319:. The chloroplast also has functionally similar beta barrel containing complexes, the best characterised of which is Toc75 of the TOC complex (Translocon at the outer envelope membrane of chloroplasts).
776:
Böcskei Z, Groom CR, Flower DR, Wright CE, Phillips SE, Cavaggioni A, et al. (November 1992). "Pheromone binding to two rodent urinary proteins revealed by X-ray crystallography".
195:, a measure of the stagger of the strands in the beta-sheet. These two parameters (n and S) are related to the inclination angle of the beta strands relative to the axis of the barrel.
242:
Up-and-down barrels are the simplest barrel topology and consist of a series of beta strands, each of which is hydrogen-bonded to the strands immediately before and after it in the
1509:
278:
Sixteen- or eighteen-stranded up-and-down beta barrel structures occur in porins, which function as transporters for ions and small molecules that cannot
157:
bacteria. It has been shown that more than 600 proteins with various function such as oxidase, dismutase, and amylase contain the beta barrel structure.
970:"Structural and functional differences in isoforms of mouse major urinary proteins: a male-specific protein that preferentially binds a male pheromone"
354:, including 2-sec-butyl-4,5-dihydrothiazole (abbreviated as SBT or DHT), 6-hydroxy-6-methyl-3-heptanone (HMH) and 2,3 dihydro-exo-brevicomin (DHB).
1298:
656:
Murzin AG, Lesk AM, Chothia C (March 1994). "Principles determining the structure of beta-sheet barrels in proteins. II. The observed structures".
621:
Murzin AG, Lesk AM, Chothia C (March 1994). "Principles determining the structure of beta-sheet barrels in proteins. I. A theoretical analysis".
191:
All beta-barrels can be classified in terms of two integer parameters: the number of strands in the beta-sheet, n, and the "shear number",
184:
containing beta barrels reverse this pattern, with hydrophobic residues oriented toward the exterior where they contact the surrounding
1502:
1261:
1240:
454:
refers to a displacement within rock perpendicular to the rock surface. In physics, the amount of displacement is referred to as
1251:
1360:
1266:
1234:
1079:
1291:
1495:
1019:"Barrel structures in proteins: automatic identification and classification including a sequence analysis of TIM barrels"
180:
and the polar residues are oriented toward the outside of the barrel on the solvent-exposed surface. Porins and other
458:, which has units of length. For shear number in barrels, displacement is measured in units of amino acid residues.
312:
122:
that twists and coils to form a closed toroidal structure in which the first strand is bonded to the last strand (
1718:
1284:
220:
316:
465:
is adjacent to just one amino acid in the neighboring strand (this assumption may not hold if, for example, a
1144:"Geometrical principles of homomeric β-barrels and β-helices: Application to modeling amyloid protofilaments"
728:"Geometrical principles of homomeric β-barrels and β-helices: Application to modeling amyloid protofilaments"
422:. Only the backbone atoms of the beta barrel are shown from each of angle of the barrel coloured from blue (
1256:
1211:
876:
Halpern M, Martínez-Marcos A (June 2003). "Structure and function of the vomeronasal system: an update".
127:
17:
455:
1723:
1518:
691:
Liu WM (January 1998). "Shear numbers of protein beta-barrels: definition refinements and statistics".
419:
474:
1091:"An evolutionarily conserved glycine-tyrosine motif forms a folding core in outer membrane proteins"
134:
used to contain liquids. Most of them are water-soluble outer membrane proteins and frequently bind
1733:
1395:
283:
461:
The determination of shear number requires the assumption that each amino acid in one strand of a
1476:
1336:
462:
339:
1222:
1728:
1410:
1307:
343:
119:
52:
1594:
208:
1102:
785:
577:
1229:" are beta-barrels (as defined in this article); "aligned" beta-sandwiches" correspond to
176:, so that the hydrophobic residues are oriented into the interior of the barrel to form a
8:
1630:
1390:
1385:
1201:
1106:
789:
581:
1375:
1247:
CATH database - folds and homologous superfamilies within the beta-barrel architecture.
1174:
1125:
1090:
1043:
1018:
994:
969:
945:
920:
901:
853:
828:
809:
758:
598:
565:
889:
542:
1650:
1542:
1424:
1400:
1178:
1166:
1130:
1075:
1048:
999:
950:
893:
858:
801:
762:
750:
708:
673:
669:
638:
634:
603:
546:
432:
225:
161:
92:
62:
905:
1645:
1568:
1355:
1158:
1120:
1110:
1038:
1030:
989:
981:
940:
932:
885:
848:
840:
813:
793:
742:
700:
665:
630:
593:
585:
538:
243:
181:
177:
57:
1671:
1635:
1537:
1115:
451:
335:
273:
255:
150:
47:
1252:
General classification and images of protein structures from Jane
Richardson lab
1676:
1604:
1573:
1532:
1429:
1350:
1345:
1326:
1143:
727:
921:"Structural basis of pheromone binding to mouse major urinary protein (MUP-I)"
153:. Porin-like barrel structures are encoded by as many as 2–3% of the genes in
1712:
1640:
1487:
1365:
1230:
1226:
968:
Armstrong SD, Robertson DH, Cheetham SA, Hurst JL, Beynon RJ (October 2005).
844:
287:
154:
146:
123:
1558:
1460:
1170:
1134:
1052:
1003:
954:
897:
862:
754:
704:
607:
550:
295:
212:
1089:
Michalik M, Orwick-Rydmark M, Habeck M, Alva V, Arnold T, Linke D (2017).
805:
712:
677:
642:
1563:
1444:
1434:
1380:
1321:
1276:
1034:
291:
135:
83:
39:
829:"Membrane protein insertion: mixing eukaryotic and prokaryotic concepts"
589:
1681:
1625:
1609:
1578:
1439:
1370:
1246:
1162:
985:
746:
529:
Wimley WC (August 2003). "The versatile beta-barrel membrane protein".
466:
427:
423:
351:
173:
169:
165:
115:
436:
229:
188:, and hydrophilic residues oriented toward the aqueous interior pore.
96:
66:
1697:
1666:
936:
797:
328:
279:
216:
142:
32:
487:. The strand order in this barrel (GFP) is: 1 6 5 4 9 8 7 10 11 3 2.
480:
403:
391:
379:
367:
347:
130:
fashion. Beta barrel structures are named for resemblance to the
87:
43:
1262:
1088:
967:
138:
131:
919:
Timm DE, Baker LJ, Mueller H, Zidek L, Novotny MV (May 2001).
1271:
509:
203:
185:
447:
cylinder. If those edges are displaced, shear is created.
76:
298:. The central pore of the protein, sometimes known as the
282:
across a cellular membrane. Such structures appear in the
1016:
775:
350:(vitamin A), while Mups bind a number of small, organic
126:). Beta-strands in many beta-barrels are arranged in an
563:
875:
564:
Lu Y, Yeung N, Sieracki N, Marshall NM (August 2009).
1017:
Nagano N, Hutchinson EG, Thornton JM (October 1999).
918:
1141:
725:
418:. The residues are labeled with residue number and
1257:Images and examples of transmembrane beta-barrels
1243:(folds 54 to 100 are water-soluble beta-barrels).
655:
620:
86:β barrel. Human retinol-binding protein bound to
1710:
450:A similar definition is found in geology, where
416:Hydrogen bonding in the beta sheet slabs of GFP
160:In many cases, the strands contain alternating
1517:
1503:
1292:
1069:
826:
1272:The OMPdb database for beta-barrel proteins
1142:Hayward S, Milner-White EJ (October 2017).
726:Hayward S, Milner-White EJ (October 2017).
719:
1510:
1496:
1306:
1299:
1285:
961:
305:
1124:
1114:
1042:
993:
944:
852:
597:
479:
202:
60:and allows sucrose to diffuse through. (
1074:(2nd ed.). New York: Garland Pub.
869:
14:
1711:
769:
566:"Design of functional metalloproteins"
528:
485:Table for calculating the shear number
1491:
1361:Transcription activator-like effector
1280:
912:
531:Current Opinion in Structural Biology
522:
827:Schleiff E, Soll J (November 2005).
690:
24:
1223:Explanation of all-beta topologies
1062:
684:
25:
1745:
1187:
1072:Introduction to protein structure
346:(Mups). RBP binds and transports
338:. Examples of the family include
313:Translocase of the outer membrane
1194:
402:
390:
378:
366:
75:
31:
1543:Structure determination methods
1241:all-beta folds in SCOP database
1010:
357:
221:2-sec-butyl-4,5-dihydrothiazole
820:
649:
614:
557:
317:Sorting and assembly machinery
237:
13:
1:
890:10.1016/S0301-0082(03)00103-5
543:10.1016/S0959-440X(03)00099-X
516:
322:
249:
1116:10.1371/journal.pone.0182016
693:Journal of Molecular Biology
670:10.1016/0022-2836(94)90065-5
658:Journal of Molecular Biology
635:10.1016/0022-2836(94)90064-7
623:Journal of Molecular Biology
469:is present). To illustrate,
141:in the barrel center, as in
7:
1070:Branden C, Tooze J (1999).
503:
262:
10:
1750:
1519:Protein tertiary structure
420:one-letter amino acid code
326:
271:
149:and are commonly found in
1690:
1659:
1618:
1587:
1551:
1525:
1469:
1453:
1409:
1335:
1314:
475:green fluorescent protein
409:Left view (270° rotation)
397:Back view (180° rotation)
385:Right view (90° rotation)
267:
107:In protein structures, a
1396:Tetratricopeptide repeat
878:Progress in Neurobiology
845:10.1038/sj.embor.7400563
340:retinol binding proteins
198:
1477:Repeated sequence (DNA)
974:The Biochemical Journal
473:will be calculated for
306:Preprotein translocases
1719:Protein tandem repeats
1308:Protein tandem repeats
705:10.1006/jmbi.1997.1501
488:
344:major urinary proteins
234:
118:(β sheet) composed of
90:(vitamin A) in blue. (
1595:Immunoglobulin domain
1267:The Lipocalin Website
483:
211:. The barrel forms a
209:major urinary protein
206:
1035:10.1110/ps.8.10.2072
42:β barrel. Bacterial
1631:Leucine-rich repeat
1391:Pentapeptide repeat
1386:Leucine-rich repeat
1107:2017PLoSO..1282016M
790:1992Natur.360..186B
590:10.1038/nature08304
582:2009Natur.460..855L
315:, and Sam50 of the
162:polar and non-polar
1454:Beads-on-a-string:
1376:Antifreeze protein
1163:10.1002/prot.25341
986:10.1042/BJ20050404
747:10.1002/prot.25341
489:
235:
1724:Protein structure
1706:
1705:
1651:Trefoil knot fold
1533:Structural domain
1485:
1484:
1425:Beta trefoil fold
1401:Trefoil knot fold
1157:(10): 1866–1881.
1081:978-0-8153-2304-4
1029:(10): 2072–2084.
980:(Pt 2): 343–350.
839:(11): 1023–1027.
784:(6400): 186–188.
741:(10): 1866–1881.
576:(7257): 855–862.
182:membrane proteins
16:(Redirected from
1741:
1691:Irregular folds:
1646:Thioredoxin fold
1569:Homeodomain fold
1512:
1505:
1498:
1489:
1488:
1356:Armadillo repeat
1301:
1294:
1287:
1278:
1277:
1198:
1197:
1182:
1148:
1138:
1128:
1118:
1085:
1057:
1056:
1046:
1014:
1008:
1007:
997:
965:
959:
958:
948:
937:10.1110/ps.52201
916:
910:
909:
873:
867:
866:
856:
824:
818:
817:
798:10.1038/360186a0
773:
767:
766:
732:
723:
717:
716:
688:
682:
681:
664:(5): 1382–1400.
653:
647:
646:
629:(5): 1369–1381.
618:
612:
611:
601:
561:
555:
554:
526:
439:
406:
394:
382:
370:
244:primary sequence
232:
178:hydrophobic core
99:
79:
69:
35:
21:
1749:
1748:
1744:
1743:
1742:
1740:
1739:
1738:
1734:Protein domains
1709:
1708:
1707:
1702:
1686:
1672:Ferredoxin fold
1655:
1636:Flavodoxin fold
1614:
1583:
1547:
1538:Protein folding
1521:
1516:
1486:
1481:
1465:
1449:
1405:
1331:
1310:
1305:
1237:classification.
1227:beta-sandwiches
1219:
1218:
1217:
1199:
1195:
1190:
1185:
1146:
1101:(8): e0182016.
1082:
1065:
1063:Further reading
1060:
1023:Protein Science
1015:
1011:
966:
962:
931:(5): 997–1004.
925:Protein Science
917:
913:
874:
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825:
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730:
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527:
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387:
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360:
331:
325:
308:
284:outer membranes
276:
274:Porin (protein)
270:
265:
256:jelly roll fold
252:
240:
224:
201:
105:
104:
103:
102:
101:
91:
80:
72:
71:
61:
56:. It sits in a
36:
23:
22:
15:
12:
11:
5:
1747:
1737:
1736:
1731:
1726:
1721:
1704:
1703:
1701:
1700:
1694:
1692:
1688:
1687:
1685:
1684:
1679:
1677:Ribonuclease A
1674:
1669:
1663:
1661:
1657:
1656:
1654:
1653:
1648:
1643:
1638:
1633:
1628:
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1616:
1615:
1613:
1612:
1607:
1605:Beta-propeller
1602:
1597:
1591:
1589:
1585:
1584:
1582:
1581:
1576:
1574:Alpha solenoid
1571:
1566:
1561:
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1553:
1549:
1548:
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1540:
1535:
1529:
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1479:
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1467:
1466:
1464:
1463:
1457:
1455:
1451:
1450:
1448:
1447:
1442:
1437:
1432:
1430:Beta-propeller
1427:
1422:
1416:
1414:
1407:
1406:
1404:
1403:
1398:
1393:
1388:
1383:
1378:
1373:
1368:
1363:
1358:
1353:
1351:Ankyrin repeat
1348:
1346:Alpha solenoid
1342:
1340:
1333:
1332:
1330:
1329:
1327:Collagen helix
1324:
1318:
1316:
1312:
1311:
1304:
1303:
1296:
1289:
1281:
1275:
1274:
1269:
1264:
1259:
1254:
1249:
1244:
1238:
1225:: "orthogonal
1200:
1193:
1192:
1191:
1189:
1188:External links
1186:
1184:
1183:
1139:
1086:
1080:
1066:
1064:
1061:
1059:
1058:
1009:
960:
911:
884:(3): 245–318.
868:
819:
768:
718:
699:(4): 541–545.
683:
648:
613:
556:
537:(4): 404–411.
520:
518:
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514:
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414:
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408:
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327:Main article:
324:
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307:
304:
272:Main article:
269:
266:
264:
261:
251:
248:
239:
236:
215:for the mouse
213:binding pocket
200:
197:
147:cell membranes
145:. Others span
120:tandem repeats
81:
74:
73:
53:S. typhimurium
37:
30:
29:
28:
27:
26:
9:
6:
4:
3:
2:
1746:
1735:
1732:
1730:
1729:Protein folds
1727:
1725:
1722:
1720:
1717:
1716:
1714:
1699:
1696:
1695:
1693:
1689:
1683:
1682:SH2-like fold
1680:
1678:
1675:
1673:
1670:
1668:
1665:
1664:
1662:
1658:
1652:
1649:
1647:
1644:
1642:
1641:Rossmann fold
1639:
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1634:
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1629:
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1608:
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1392:
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1379:
1377:
1374:
1372:
1369:
1367:
1366:Beta solenoid
1364:
1362:
1359:
1357:
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1352:
1349:
1347:
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1260:
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1248:
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1242:
1239:
1236:
1232:
1231:beta-sandwich
1228:
1224:
1221:
1220:
1215:
1214:
1213:
1207:
1203:
1180:
1176:
1172:
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1077:
1073:
1068:
1067:
1054:
1050:
1045:
1040:
1036:
1032:
1028:
1024:
1020:
1013:
1005:
1001:
996:
991:
987:
983:
979:
975:
971:
964:
956:
952:
947:
942:
938:
934:
930:
926:
922:
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903:
899:
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687:
679:
675:
671:
667:
663:
659:
652:
644:
640:
636:
632:
628:
624:
617:
609:
605:
600:
595:
591:
587:
583:
579:
575:
571:
567:
560:
552:
548:
544:
540:
536:
532:
525:
521:
511:
508:
507:
501:
499:
493:
486:
482:
478:
476:
472:
468:
464:
459:
457:
453:
448:
438:
434:
429:
425:
421:
417:
405:
393:
381:
369:
355:
353:
349:
345:
341:
337:
330:
320:
318:
314:
303:
301:
297:
293:
289:
288:gram-negative
285:
281:
275:
260:
257:
247:
245:
231:
227:
222:
218:
214:
210:
205:
196:
194:
189:
187:
183:
179:
175:
171:
167:
163:
158:
156:
155:Gram-negative
152:
148:
144:
140:
137:
133:
129:
125:
124:hydrogen bond
121:
117:
113:
110:
98:
94:
89:
85:
78:
68:
64:
59:
55:
54:
49:
45:
41:
34:
19:
1599:
1588:All-β folds:
1559:Helix bundle
1552:All-α folds:
1461:Sushi domain
1419:
1210:
1209:
1208:profile for
1205:
1154:
1150:
1098:
1094:
1071:
1026:
1022:
1012:
977:
973:
963:
928:
924:
914:
881:
877:
871:
836:
833:EMBO Reports
832:
822:
781:
777:
771:
738:
734:
721:
696:
692:
686:
661:
657:
651:
626:
622:
616:
573:
569:
559:
534:
530:
524:
497:
494:
490:
484:
470:
460:
456:shear strain
449:
445:
415:
358:Shear number
332:
309:
299:
296:mitochondria
292:chloroplasts
277:
253:
241:
192:
190:
159:
128:antiparallel
111:
108:
106:
51:
1600:Beta barrel
1564:Globin fold
1445:WD40 repeat
1435:Kelch motif
1420:Beta barrel
1381:HEAT repeat
1322:Coiled coil
1212:Beta barrel
342:(RBPs) and
238:Up-and-down
174:amino acids
170:hydrophobic
166:hydrophilic
136:hydrophobic
109:beta barrel
18:Beta-barrel
1713:Categories
1660:α+β folds:
1626:TIM barrel
1619:α/β folds:
1610:Beta helix
1579:Death fold
1440:TIM barrel
1371:Beta helix
517:References
467:beta bulge
463:beta sheet
428:C-terminus
426:) to red (
424:N-terminus
373:Front view
352:pheromones
323:Lipocalins
290:bacteria,
250:Jelly roll
143:lipocalins
116:beta sheet
112:(β barrel)
46:-specific
1698:Conotoxin
1667:DNA clamp
1470:See also:
1337:Elongated
1233:folds in
1179:206410314
763:206410314
500:, is 14.
329:Lipocalin
217:pheromone
1315:Fibrous:
1171:28646497
1151:Proteins
1135:28771529
1095:PLOS ONE
1053:10548053
1004:15934926
955:11316880
906:31122845
898:12951145
863:16264426
755:28646497
735:Proteins
608:19675646
551:12948769
504:See also
440:)
263:Examples
233:)
207:A mouse
100:)
70:)
58:membrane
1526:General
1202:Scholia
1126:5542473
1103:Bibcode
1044:2144152
995:1276933
946:2374202
854:1371041
814:4362015
806:1279439
786:Bibcode
713:9466929
678:8126727
643:8126726
599:2770889
578:Bibcode
348:retinol
280:diffuse
139:ligands
132:barrels
88:retinol
44:sucrose
1411:Closed
1204:has a
1177:
1169:
1133:
1123:
1078:
1051:
1041:
1002:
992:
953:
943:
904:
896:
861:
851:
812:
804:
778:Nature
761:
753:
711:
676:
641:
606:
596:
570:Nature
549:
512:(2011)
300:eyelet
294:, and
268:Porins
186:lipids
151:porins
84:strand
40:strand
1206:topic
1175:S2CID
1147:(PDF)
902:S2CID
810:S2CID
759:S2CID
731:(PDF)
510:OMPdb
452:shear
336:calyx
199:Types
114:is a
50:from
48:porin
1235:SCOP
1167:PMID
1131:PMID
1076:ISBN
1049:PMID
1000:PMID
951:PMID
894:PMID
859:PMID
802:PMID
751:PMID
709:PMID
674:PMID
639:PMID
604:PMID
547:PMID
437:1RRX
430:). (
254:The
230:1MUP
168:and
97:1RBP
67:1A0S
1159:doi
1121:PMC
1111:doi
1039:PMC
1031:doi
990:PMC
982:doi
978:391
941:PMC
933:doi
886:doi
849:PMC
841:doi
794:doi
782:360
743:doi
701:doi
697:275
666:doi
662:236
631:doi
627:236
594:PMC
586:doi
574:460
539:doi
433:PDB
286:of
226:PDB
223:. (
93:PDB
63:PDB
38:18-
1715::
1173:.
1165:.
1155:85
1153:.
1149:.
1129:.
1119:.
1109:.
1099:12
1097:.
1093:.
1047:.
1037:.
1025:.
1021:.
998:.
988:.
976:.
972:.
949:.
939:.
929:10
927:.
923:.
900:.
892:.
882:70
880:.
857:.
847:.
835:.
831:.
808:.
800:.
792:.
780:.
757:.
749:.
739:85
737:.
733:.
707:.
695:.
672:.
660:.
637:.
625:.
602:.
592:.
584:.
572:.
568:.
545:.
535:13
533:.
435::
246:.
228::
219:,
172:)
95::
82:8-
65::
1511:e
1504:t
1497:v
1413::
1339::
1300:e
1293:t
1286:v
1216:.
1181:.
1161::
1137:.
1113::
1105::
1084:.
1055:.
1033::
1027:8
1006:.
984::
957:.
935::
908:.
888::
865:.
843::
837:6
816:.
796::
788::
765:.
745::
715:.
703::
680:.
668::
645:.
633::
610:.
588::
580::
553:.
541::
498:S
471:S
193:S
164:(
20:)
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