Comparative Study of Elastic Network Model and Protein Contact Network for Protein Complexes: The Hemoglobin Case

<div>Guimerà-Amaral Cartography for <svg height="9.01194pt" id="M276" style="vertical-align:-0.04981995pt" version="1.1" viewbox="-0.0498162 -8.96212 8.41168 9.01194" width="8.41168pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"><g transform="matrix(.013,0,0,-0.013,0,0)"><path d="M620 675H597C578 656 570 650 541 650H144C112 650 104 653 94 675H72C59 618 42 552 23 493L53 491C71 534 88 564 105 585C124 608 144 615 238 615H290L197 121C182 40 174 34 88 28L82 0H361L367 28C275 34 266 38 281 121L374 615H441C522 615 543 608 553 583C562 560 566 531 565 493L597 494C603 551 612 629 620 675Z" id="g113-85"></path><glyph.data ascent="3473" descent="-2876" horiz-adv-x="637" vert-adv-y="637"></glyph.data></g></svg>-Hb: very few nodes are classified as hubs (<svg height="8.8423pt" id="M277" style="vertical-align:-0.2064009pt" version="1.1" viewbox="-0.0498162 -8.6359 14.5446 8.8423" width="14.5446pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"><g transform="matrix(.013,0,0,-0.013,0,0)"><path d="M610 18C585 26 567 34 540 68C517 97 499 128 476 171C452 215 425 276 413 304C496 332 570 394 570 494C570 555 545 595 509 619S419 650 364 650H139L133 622C216 615 219 612 203 527L129 132C112 40 105 36 23 28L17 0H279L285 28C199 34 194 40 211 132L239 284H284C320 284 334 275 351 236C374 182 394 140 420 93C459 23 495 -1 592 -8H600L610 18ZM480 485C480 424 449 372 403 342C374 323 338 316 293 316H245L291 562C296 589 301 601 311 608S337 618 358 618C432 618 480 575 480 485Z" id="g113-83"></path><glyph.data ascent="3473" descent="-2876" horiz-adv-x="627" vert-adv-y="627"></glyph.data></g><g transform="matrix(.013,0,0,-0.013,8.151,0)"><path d="M153 550H386L412 615L406 623H120L82 318C104 327 142 338 184 338C294 338 347 275 347 187C347 112 305 39 221 39C160 39 119 71 97 89C88 97 80 96 71 90C59 80 50 67 49 57C48 45 52 36 66 23C80 9 123 -12 169 -12C221 -11 288 15 342 59C403 109 431 165 431 225C431 308 366 395 238 395C212 395 165 379 127 364L153 550Z" id="g113-54"></path><glyph.data ascent="3473" descent="-2876" horiz-adv-x="480" vert-adv-y="480"></glyph.data></g></svg>), but more than for <svg height="8.8423pt" id="M278" style="vertical-align:-0.2064009pt" version="1.1" viewbox="-0.0498162 -8.6359 8.28119 8.8423" width="8.28119pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"><g transform="matrix(.013,0,0,-0.013,0,0)"><path d="M610 18C585 26 567 34 540 68C517 97 499 128 476 171C452 215 425 276 413 304C496 332 570 394 570 494C570 555 545 595 509 619S419 650 364 650H139L133 622C216 615 219 612 203 527L129 132C112 40 105 36 23 28L17 0H279L285 28C199 34 194 40 211 132L239 284H284C320 284 334 275 351 236C374 182 394 140 420 93C459 23 495 -1 592 -8H600L610 18ZM480 485C480 424 449 372 403 342C374 323 338 316 293 316H245L291 562C296 589 301 601 311 608S337 618 358 618C432 618 480 575 480 485Z" id="g113-83"></path><glyph.data ascent="3473" descent="-2876" horiz-adv-x="627" vert-adv-y="627"></glyph.data></g></svg>/O<sub>2</sub> complex, again close to the active site. Non-hub kinless nodes (<svg height="8.8423pt" id="M279" style="vertical-align:-0.2064009pt" version="1.1" viewbox="-0.0498162 -8.6359 14.5446 8.8423" width="14.5446pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"><g transform="matrix(.013,0,0,-0.013,0,0)"><path d="M610 18C585 26 567 34 540 68C517 97 499 128 476 171C452 215 425 276 413 304C496 332 570 394 570 494C570 555 545 595 509 619S419 650 364 650H139L133 622C216 615 219 612 203 527L129 132C112 40 105 36 23 28L17 0H279L285 28C199 34 194 40 211 132L239 284H284C320 284 334 275 351 236C374 182 394 140 420 93C459 23 495 -1 592 -8H600L610 18ZM480 485C480 424 449 372 403 342C374 323 338 316 293 316H245L291 562C296 589 301 601 311 608S337 618 358 618C432 618 480 575 480 485Z" id="g113-83"></path><glyph.data ascent="3473" descent="-2876" horiz-adv-x="627" vert-adv-y="627"></glyph.data></g><g transform="matrix(.013,0,0,-0.013,8.151,0)"><path d="M456 178V225H360V632H320C217 496 115 347 20 206V178H280V106C280 40 276 34 189 27V0H445V27C364 34 360 39 360 106V178H456ZM280 225H82C149 335 214 431 278 520H280V225Z" id="g113-53"></path><glyph.data ascent="3473" descent="-2876" horiz-adv-x="480" vert-adv-y="480"></glyph.data></g></svg>) lie on the interface between chains. Similar results hold for <svg height="8.8423pt" id="M280" style="vertical-align:-0.2064009pt" version="1.1" viewbox="-0.0498162 -8.6359 14.5446 8.8423" width="14.5446pt" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"><g transform="matrix(.013,0,0,-0.013,0,0)"><path d="M610 18C585 26 567 34 540 68C517 97 499 128 476 171C452 215 425 276 413 304C496 332 570 394 570 494C570 555 545 595 509 619S419 650 364 650H139L133 622C216 615 219 612 203 527L129 132C112 40 105 36 23 28L17 0H279L285 28C199 34 194 40 211 132L239 284H284C320 284 334 275 351 236C374 182 394 140 420 93C459 23 495 -1 592 -8H600L610 18ZM480 485C480 424 449 372 403 342C374 323 338 316 293 316H245L291 562C296 589 301 601 311 608S337 618 358 618C432 618 480 575 480 485Z" id="g113-83"></path><glyph.data ascent="3473" descent="-2876" horiz-adv-x="627" vert-adv-y="627"></glyph.data></g><g transform="matrix(.013,0,0,-0.013,8.151,0)"><path d="M412 140C382 77 369 73 315 73H129L270 222C362 320 402 379 402 466C402 571 322 635 234 635C177 635 130 609 99 576L42 495L64 475C90 514 133 568 201 568C274 568 318 519 318 435C318 349 255 267 193 193C144 135 87 78 32 23V0H405C417 45 427 89 440 131L412 140Z" id="g113-51"></path><glyph.data ascent="3473" descent="-2876" horiz-adv-x="480" vert-adv-y="480"></glyph.data></g></svg>-Hb; see Supplementary Figure S6.</div>

BioMed Research International

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Figure 9

Figure 9: Comparative Study of Elastic Network Model and Protein Contact Network for Protein Complexes: The Hemoglobin Case 